Mark Johnson


Research Classification

Research Interests

Carbon cycle
Climate Changes and Impacts
data science
Ecology and Quality of the Environment
Fresh Water
Ground Water and Water Tables
Hydrological Cycle and Reservoirs
Land and Soil
land use
Running Water Hydrosystem
Water and Sustainability

Relevant Degree Programs

Affiliations to Research Centres, Institutes & Clusters



Our work in ecohydrology and watershed biogeochemistry includes field-based research involving real-time measurements of water quantity and quality which we complement through GIS-based modeling, laboratory analysis and stakeholder input. The overarching goal is to leverage this research towards the development of more sustainable land-use practices and urban systems.

Research Methodology

Data acquisition systems
Watershed modeling
Environmental measurements and monitoring


Master's students
Doctoral students
Postdoctoral Fellows

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Graduate Student Supervision

Doctoral Student Supervision (Jan 2008 - April 2022)
Community-based stream and groundwater monitoring and future change impact modelling of a socio-ecohydrological system to inform drought adaptation in the seasonally-dry tropics (2019)

With a changing climate and a growing population, droughts are becoming more frequent in many watersheds across the world, necessitating new approaches to improve water security in communities. Drought is typically caused by a combination of hydrological and social drivers. In this thesis, I apply the emerging framework of socio-hydrology (coupled human-water systems). Specifically, the objective of this thesis is to assess current and future socio- and hydrological dynamics and impacts on surface water and groundwater supplies with the goal of informing drought adaptation and improving water security. I focused hereby on two drought-prone rural watersheds in the seasonally-dry tropics of Costa Rica. Using a community-based approach, I implemented a hydrological monitoring network of streams and groundwater with open-source data loggers, and worked with local communities to assemble societal water use data. I then synthesized the watersheds in a hydrological model and assessed current social (water use) and hydrological vulnerabilities to drought. Results showed that communities dominantly relied on groundwater supplies, and that a temporal mismatch between water availability and needs, high domestic water use, and increasing extraction rates are increasing pressure on groundwater. Results also indicated high streamflows during the wet season, and thus a potential to increase surface water use while streamflows are high. Next, I explored the impacts of the El Niño Southern Oscillation (ENSO), future climate change and water use change on water resources in the study watersheds. During an extreme El Niño, groundwater recharge and streamflow decreased by 60% relative to ENSO Neutral. I also found that future climate change may lead to groundwater storage decline, especially if combined with high population growth. In the seasonally-dry tropics, wet season rainfall is essential for recharging groundwater that serves as primary water supply during long dry seasons. Therefore, I developed a novel ‘groundwater recharge indicator’ as a tool to support water managers to respond adaptively to reduced wet season rainfall and increase socio-hydrological resilience to seasonal drought. Overall, this thesis contributes to the field of socio-hydrology and provides novel approaches to improve water security under drought in the seasonally-dry tropics.

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Harmonizing water footprint assessments for agricultural production in Southern Amazonia (2018)

No abstract available.

Biochar for the Brazilian Cerrado: contributions to soil quality and plant growth (2017)

Arenosols (sandy soils) in the Cerrado region of Mato Grosso, Brazil are increasingly used for maize production. These soils are typically nutrient poor with low soil water retention. Since biochar has been shown to improve both nutrient and water retention, this thesis aimed to evaluate biochar effect on physical and chemical properties of a Cerrado Arenosol using four biomass wastes (cotton husks, swine manure, eucalyptus sawmill residue, and sugarcane filtercake) pyrolyzed at three temperatures (400°, 500°, 600°C). These biomass wastes were chosen based on their prevalence in the state of Mato Grosso and their environmental impact. Three greenhouse experiments were carried out with the following objectives: 1) to assess the effects of biochar feedstock type and temperature of pyrolysis on soil water retention; 2) to examine the effect of different biochars on soil nutrients and maize growth applied to soil at different rates, and 3) to observe how different biochar feedstocks and temperatures of pyrolysis affect DOC and NO₃- leaching from a Cerrado Arenosol. All the biochars showed potential to reduce water drainage in the soil compared to the control (no biochar). At application rates 1-4% w/w, filtercake biochar led to the highest mean biomass compared to the other biochars. Eucalyptus biochar did not contribute much to soil fertility, but filtercake biochar led to high soil nutrient concentrations, e.g. Ca, Fe, Mn. Although swine manure biochar was rich in nutrients, low plant biomass in the cotton and swine manure biochar treatments was likely due to higher pH, salinity, and/or excessive water retention. Lastly, DOC and NO₃- concentrations were low in leachate from soils with filtercake and eucalyptus biochars, and high in leachate from soils with cotton and swine manure biochars. This thesis provides an outlook of the agronomic potential of these biochars. Further analyses, such as their effect on soil biological properties, are required to develop well-rounded biochar-soil management practices for Cerrado Arenosols.

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From streams to citizens: a multi-lens investigation of water quality through carbon cycles and participation within water science and policy (2017)

Water management approaches that are scientifically sound and societally relevant are critical, given the myriad demands and threats posed to this resource and its necessity for environmental and human life. This thesis reflects the inherently complex and multifaceted nature of water management by investigating issues of water quality, as well as societal participation within science outlining the health of water resources, and policy that determines admissible human impacts.First, the technical details of deploying in situ water quality monitoring networks are examined, given challenges of installing sensitive and costly sensors within remote and physically dynamic stream environments. A year of high frequency measurements explicates the necessity of measuring concentrations at adequate time intervals to accurately calculate fluxes of dissolved organic carbon (DOC).Secondly, these spectrophotometric approaches were used to investigate how forest harvest affects in-stream DOC biogeochemistry within a small headwater stream on Vancouver Island, British Columbia. Forest harvest has a large impact on catchment biogeochemistry and hydrology. Harvest increases DOC concentration and flux within the stream. It also alters the chemical composition of DOC, signifying impacts on the catchment scale mechanisms by which DOC is created and transported.Thirdly, the impacts of citizen participation on scientific data outcomes within the burgeoning field of citizen science are detailed. Six critical lessons learned were distilled from a citizen science water quality monitoring program (concerning DOC concentration and characteristics). Scientific data was used alongside qualitative vignettes to explicate the importance of citizen perspectives, contextual knowledge, and motivations for involvement on critical data outcomes.Lastly, the process and outcomes of public participation through consultation in the creation of provincial-level water policy are discussed. The extensive public consultation process undertaken during the modernization of BC’s Water Sustainability Act was used to examine what was expressed during consultation, and how this compared to the contents of the Act. Differences between consultation outcomes and Act contents (especially related to water allocation) bring to bear questions regarding the function of consultation within participatory policy processes, including how consultation was (and should be) used, and the possible influence of elite groups.

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Impacts of biochar application to a Douglas-fir forest soil on greenhouse gas fluxes and water quality (2017)

Forest management for carbon sequestration is a valuable tool to combat rising greenhouse gas (GHG) concentrations in the Earth’s atmosphere. This thesis examined the use of biochar, a product of the thermal decomposition of waste organic matter in a reduced oxygen environment (i.e. pyrolysis) that is applied to soil, as an option for increasing carbon sequestration in a Coastal Douglas-fir forest soil in British Columbia when applied with and without urea fertilizer at 200 kg N ha-¹. Biochar produced from Douglas-fir forestry slash materials was used in this study to address this from a systems-based perspective. A soil incubation study showed that biochar application at high rates (10% oven dry soil basis) significantly increased CO₂ and N₂O emissions when applied without fertilizer and at both low (1%) and high rates (10%) decreased CH₄ consumption without fertilization. In terms of carbon dioxide equivalent emissions (CO₂e), it was shown that CO₂ accounted for >98% from all treatments. In a field study, GHG fluxes were measured after application of 5 t ha-¹ of biochar to a Douglas-fir forest soil in the first year followed by urea-N fertilization in the second year. The results showed that 5 t ha-¹ of biochar had little effect on GHG fluxes and their total CO₂e fluxes. Applying biochar prior to fertilizer application following industry-standard practices did not significantly change treatment CO₂e fluxes. It was concluded that low rates of biochar application to this forest soil would improve soil C sequestration with or without fertilization. In the field and laboratory experiments, soil pore water was extracted and analyzed for C and N concentrations and dissolved organic carbon using spectral indices. The results showed that low biochar application rates could be beneficial for both increasing C-sequestration and N-retention. Changes in spectral indices measured in the laboratory suggested that alterations in the dissolved organic matter pool could lead to changes in GHG emissions due to changing substrate supply for microbes as application rates increased. There is a recognized need for further studies prior to large-scale industrial applications; however, as result of this work it is possible to provide recommendations for large-scale pilot studies.

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Closing the carbon loop in sugarcane bioethanol: effects of filtercake biochar amendment on soil quality, leaching and carbon utilization (2014)

Commodity prices and rural development in Brazil are driving the rapid conversion of the Cerrado biome, a highly diverse ecosystem with nutrient-poor soils. The expanding agricultural footprint includes sugarcane for bioethanol production, which boasts one of the highest net energy yields of commercial biofuels. However, energetic assessments fail to consider ecosystem costs, including soil degradation and impacts on water quality through the release of organic effluents. This thesis examined the use of charcoal or biochar made of ‘waste’ biomass (filtercake) as a soil amendment to reduce soil carbon (C) loss and water quality impairment. The effect of biochar on the leaching of a liquid waste with high eutrophication potential, vinasse, was also examined. Soil amendment with filtercake biochar improved soil pH, cation exchange capacity (CEC), nutrient availability (P, K, Mg, Ca, Mg, Fe, Mn, and Zn), and water retention. Amendment with filtercake biochar rather than raw filtercake also greatly decreased CO₂ loss to rapid mineralization. Furthermore, biochar amendment decreased the loss of dissolved organic carbon (DOC) from a cultivated Ferralsol, with or without co-application of vinasse, through preferential retention of larger and more complex, humified DOC species. In contrast, biochar did not attenuate nitrate (NO₃-) leaching. Finally, δ¹³C isotope analyses were used to examine the effect of raw vs. pyrolyzed residues on C turnover in an uncultivated soil, which suggested that whereas raw filtercake appeared to be mineralized preferentially over native soil organic carbon (SOC), biochar application appeared to provoke mineralization of native SOC. Overall, this project suggest that filtercake biochar may represent a valuable opportunity to better manage solid and liquid organic agricultural wastes in bioethanol production, with the potential to close nutrient loops and improve soil quality. However, further work is required to better understand the effect of filtercake biochar on soil C turnover and its long-term stability.

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Master's Student Supervision (2010 - 2021)
Spatial and temporal variation in natural organic matter quantity and quality across a second growth forested drinking water supply area on Vancouver Island, BC (2021)

Most drinking water in Canada originates in forested headwaters, therefore drinking water security is tied to forest management for many communities. Monitoring source water quality is crucial to a multi-barrier approach to clean drinking water. This research established a stream water sampling program across a second-growth forested drinking water supply area (Greater Victoria, British Columbia, Canada) to evaluate spatiotemporal patterns and variance in natural organic matter (NOM). Over sixteen months (October 2018 to February 2020), 426 stream water samples were collected from twelve sites (ranging from 9.6 to 37 km², elevation 215 to 870 m a.s.l) and analyzed for NOM quality (via UV-Vis absorbance) and quantity (as dissolved organic carbon, DOC). Mean sub-basin DOC concentrations ranged from 4.2 ± 1.8 mg/L⁻¹ to 9.9 ± 3.4 mg/L⁻¹ (DOC range 1.64 - 19.1 mg/L⁻¹). Six of the twelve sites in Leech River watershed (~96 km²) were equipped with vertical passive sampling racks to evaluate rising hydrograph limb NOM dynamics. Hydrologic connectivity to terrestrial source pools increased throughout wet seasons and antecedent wetness was important for stream NOM molecular quality, which shifted from predominantly aliphatic in the dry-season to predominantly aromatic in the wet-season. Sample sub-sets were evaluated for drinking water treatability parameters (n = 8) and total metals contents (n = 42). DOC was correlated with several metals (R² values for Hg: 0.99; Al: 0.81; Fe: 0.72; Cu: 0.47; Ba: 0.25; Mn: 0.21), evidence that aqueous NOM is indeed a master variable important for contaminant transport. More than specific UV absorbance (SUVA₂₅₄) or DOC concentration, the spectral absorbance coefficient at 254 nm (SAC254) was well correlated to disinfection byproduct formation-potential (total trihalomethanes, r = 0.9882; and total haloacetic acids, r = 0.9927). Approximately 80% of the time, DOC concentration peaked with stream stage. Random Forest variable importance measure (RF VIM) identified warm and wet conditions as key drivers for NOM dynamics. RF VIM showed that forest age and harvest history were important predictor variables for NOM aromaticity and molecular size, but that subsurface parent material was a more important driver for NOM quantity and quality.

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Forest harvest and water treatability: Analysis of dissolved organic carbon in headwater streams of contrasting forest harvest history during base flow and storm flow (2020)

No abstract available.

Modeling dam removal in a mountain meadow with MODFLOW-NWT (2019)

No abstract available.

Determining gas transfer velocities and CO2 evasion fluxes from streams using carbon dioxide as a tracer (2017)

Evasion of carbon dioxide (CO₂) from headwater streams is a dominant process controlling the fate of terrestrially-derived carbon (C) in inland waters. However, methodological limitations associated with determining the gas transfer velocity of carbon dioxide (kCO₂) in headwater streams inhibit efforts to accurately quantify CO₂ emissions. In this thesis, I present a proof of concept for a tracer gas method that mitigates common issues associated with conventional methods for determining kCO₂. In this method, a datalogger controls in situ stream sensors that measure the partial pressure of CO₂ (pCO₂) and other stream parameters as well as a solenoid valve connected to a compressed CO₂ cylinder. Automated injections of CO₂ were made via an aquatic diffuser located on the stream bed. Infrared gas-analyzing (IRGA) CO₂-type sensors enclosed in waterproof, gas-permeable membranes located downstream from the diffuser continuously measured aqueous pCO₂ and equilibrate to elevated values during CO₂ injections. The difference between upstream and downstream pCO₂ values during CO₂ injection relative to pre-injection concentrations permitted calculation of both the CO₂ flux from the reach and kCO₂. This method improves upon conventional methods due to its automation, in situ measurement, and use of CO₂ as a tracer rather than another gas, thereby reducing analytical error and increasing the frequency and timing with which measurements can be made relative to conventional methods. I tested this method in a headwater stream in southwestern British Columbia. I calculated kCO₂ and continuous CO₂ emissions from the reach and compared both datasets to hydrogeomorphic parameters as well as values in the literature. Values of kCO₂ were generally above the average values reported in the literature, but they corresponded well to values reported for steep, turbulent headwater streams. Values of kCO₂ varied in relation to discharge, flow velocity, and stream temperature. CO₂ emissions from the stream were highest during high flow events. Headwater streams, which have been shown to be "hotspots" for CO₂ emissions, can also be considered as exhibiting "hot moments" of CO₂ evasion.

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Net ecosystem carbon balance for a peat bog undergoing restoration by integrating flux tower and aquatic flux measurements (2017)

Peatlands are wetlands where gross primary production exceeds organic matter decomposition causing an accumulation of partially decomposed matter, also called peat. Peat ecosystems can accumulate more carbon (C) than tropical rainforests. However, dissolved fluxes of C (as dissolved organic carbon (DOC), carbon dioxide (CO₂) and methane (CH₄)) must also be considered to determine if these ecosystems are net sinks or sources of greenhouse gases (GHGs) to the atmosphere. This research was conducted in Burns Bog, Delta, BC, Canada, one of the largest bogs on the west coast of the Americas, but which has been heavily impacted by a range of human activities. Currently, ecological restoration efforts are underway by a large-scale ditch blocking program, with the aim of re-establishing water table conditions that promote peat accumulation. Here I present data on ecosystem-scale fluxes of CO₂ and CH4 determined by eddy covariance (EC), together with data on (i) evasion fluxes of CO₂ and CH₄ from the water surface, and (ii) the flux and characteristics of DOC in water draining Burns Bog. The net ecosystem carbon balance (NECB) was determined as the sum of EC fluxes and DOC export. Concentrations of dissolved CO₂ and CH₄ were determined by headspace equilibration, and evasion rates from the water surface were quantified and used to estimate the role of the hydrosphere in the ecosystem-scale measurements. Water samples collected from five saturated areas in the flux tower footprint were analyzed for DOC concentrations and characteristics. Satellite imaging showed that during the dry season 10% of the area was covered by water, while on the wet season, it was 60%. The hydrosphere was found to be a continual C source, emitting 271 g C m-² yr-¹. NECB was found to be -98 g C m-² yr-¹. DOC export was found to offset about 60% of the apparent net C emissions determined by EC during the wet season and 3% of the net C uptake during the dry season, indicating that the EC measurements by themselves underestimate C emissions during the wet season and overestimate C accumulation in the dry season by not accounting for DOC drainage.

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Looking Past the Present Waste: Path Dependencies in Municipal Solid Waste Management in the US and European Union (2014)

Incineration of municipal solid waste practiced in Europe has been noted as a best practice, and if not for NIMBYism, it is one that the US could adopt more broadly. At present waste-to-energy technologies, such as incineration, are used to manage 24% of municipal solid waste generated per year in the EU, while the US incineration is used to manage slightly under 12% of municipal solid waste per year. Additionally, incineration in the EU has increased over the past 20 years whereas incineration in the US has been on a lingering decline over this same time period. However, the use of incineration was once greater in the US than it is today in the EU. This study analyzed the reasons for this divergence in incineration use through investigation of historical events beginning in the early 1800s in both regions. Identification and analysis of key drivers and critical junctures in the US and Europe are compared. Over time, these events created path dependencies which explain the evolution of municipal solid waste management in the US and Europe. Particularly important path dependent drivers of this evolution include local control, availability of funds, and availability of resources. The historical analysis indicates that European municipalities having a long history of local control, the financial capacity to fund infrastructure and service projects, and an awareness of benefits gained from waste-to-energy technology have resulted in the increased adoption of municipal solid waste incineration. Conversely, US municipalities had local authority eroded and constrained over time, had a lack of financial capacity and assistance to fund municipal projects, and also had access to relatively abundant land and fossil fuel resources. The result was the decline of reliance on incineration in the US since 1960. An understanding of the importance of path dependencies in shaping current renewable technology adoption, such as waste-to-energy, can better inform other policy discussions including climate change.

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The effects of biochar application on carbon dioxide and methane soil surface fluxes (2014)

Soils contain the largest terrestrial organic carbon (C) stock, representing two-thirds or more of terrestrial C. Soils can act as a source or sink for carbon dioxide (CO₂) and methane (CH₄). One common technique for studying soil surface effluxes of CO₂ (FCO₂) and of CH₄ (FCH₄) is the soil chamber. This involves placing an enclosure over the soil surface and measuring the change in headspace concentration of the gas of interest over time. Due to the air-filled pore spaces within the near-surface soil, and adsorption of gases of interest onto chamber walls, the effective volume (Veff) of the chamber which contributes to FCO₂ and FCH₄ measurements is generally higher than the geometric volume (Vg) of the chamber. It is necessary that Veff be known in order to estimate fluxes accurately. This study coupled a flow-through non-steady-state automated chamber system to a laser-based cavity ring-down spectrometer (CRDS) to estimate Veff of the chamber system using separate standard additions of CO₂ and CH₄ calibration gases. The system was then mounted onto soil cylinders which had been filled with a forest soil from Vancouver Island, British Columbia, Canada. There has been recent interest in the ability of biochar to provide multiple environmental benefits upon application to soil, including the long-term sequestration of C. There are conflicting studies as to the effect of biochar on FCO₂ and FCH₄ and overall greenhouse gas (GHG) emissions.After making background measurements of FCO₂ and FCH₄ in soil columns, biochar was applied to one of the columns and the resulting FCO₂ and FCH₄ were measured. The results from this study showed that the coupling of the CRDS to the automated chamber system proved to be successful. The estimated Veff during CO₂ and CH₄ calibration gas injections agreed with past studies as the Veff was 5 to 10% larger than the geometric volume of the chamber. Following biochar application, the amended soil produced 36.9% more CO₂ and consumed 20.4% less CH₄ than the control over the four month experiment. The results showed that soil water content was an important factor in controlling FCO₂ and FCH₄ following biochar amendment.

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Land use effects on green water fluxes in Mato Grosso, Brazil (2011)

The blue water - green water paradigm has been increasingly used to describe water resources. Blue water represents liquid flows in rivers or aquifers, while green water (GW) represents vapour exchanges with the atmosphere either as evaporation from soil or as transpiration from plants. This study assesses the impacts of land use change on GW fluxes in the Brazilian state of Mato Grosso, an ideal candidate for the study of GW in light of recent deforestation for pasture and soybean expansion, and the near complete reliance of its agricultural land base on precipitation as the GW source. Fluxes were estimated for 2000-2009 by combining the MODerate Resolution Imaging Spectroradiometer (MODIS) evapotranspiration product with forest cover change from Brazil’s National Institute of Space Research (INPE), as well as guidelines from the Food and Agriculture Organization (FAO) to model soybean, maize, sugar cane, cotton and pasture GW. In 2000, forest cover represented one third of the state’s land base and returned half of the state’s water vapour to the atmosphere. Annual total GW volumes decreased by 10 % between 2000 and 2009 at a rate of 16.2 km³y⁻¹ per year. Deforestation explained up to 27 % of variance in annual total volumes while agricultural expansion, as cropland and pasture, explained up to 20 %. Cropland GW doubled within the study time period, 75 % to 83 % of which constituted soybean GW. Pasture GW was 5 times larger than soybean GW and offset the increase in cropland GW. The greatest uncertainty lies in the role played by residual land use GW fluxes which were attributed to Brazilian savanna (cerrado), the Pantanal wetland, as well as unaccounted agricultural land left as fallow.

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Changing with the flow: an analysis of water supply and demand in a subwatershed of the Okanagan Basin, British Columbia (2010)

Surface water is critical for meeting water needs in British Columbia’s Okanagan Basin, but the timing and magnitude of its availability is being altered through climate and land use changes and growing water demand. WEAP, an integrated water management model, was used to consider future scenarios for water supply and demand in an unregulated and a reservoir-supported stream that supply the District of Peachland. Potential changes to the magnitude and timing of streamflow were evaluated in response to the following scenarios: (i) climate change (derived from the HadCM3 and CGCM2 GCMs for the 2020s and 2050s), (ii) a simulated prolonged drought, (iii) land cover change resulting from a Mountain Pine Beetle (MPB) outbreak, and (iv) combinations of these conditions. These changes, in combination with likely demand increases and reservoir operating rules were evaluated in terms of stress on water availability for human use and aquatic life. Results demonstrate that anticipated future climate conditions will critically reduce streamflow relative to demand (societal and ecological) in at least a few months of “normal” and “dry” years. On the unregulated creek, an earlier recession of peak spring snowmelt, accompanied by higher demands at the beginning of the summer outdoor watering season as early as the 2020s, reduced the ability to meet downstream needs. On the regulated stream, two “very dry” years under a climate change scenario resulted in deficits for municipal water users under a higher reservoir release scenario. In all scenarios, even with the higher flows expected under the MPB scenario, some combinations of demand, reservoir operations and climate variability resulted in less than optimal conditions for instream ecological flow needs. Beyond the implications for the District of Peachland, this work demonstrates a method of using an accessible modeling tool for integrating knowledge from the fields of climate science, forest hydrology, water systems management and stream ecology to aid in water and land management decision-making.

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