With widespread ongoing urbanization and as climate change continues, the importance of protecting the water quality of streams and lakes is intensifying. However, while many water quality constituents in lakes and rivers are of overall interest, water temperature is a ‘key’ variable as temperature influences mixing within a waterbody, influences the acceptability of the habitat for flora and fauna, and serves as a guide to the general health of a stream. To enable the assessment, a physics-based, deterministic hydraulic and heat-balance modeling procedure using the combination of MIKE SHE, MIKE HYDRO and ECO Lab is described to assess heat transfer magnitudes in portions of the Credit River, Ontario. Changes in instream temperature regimes are examined, including both frequency and spatial extent, providing insights into the impacts of urbanization in terms of seasonal temperature shifts arising from land use changes. For flow and temperature regimes, Nash–Sutcliffe model efficiency coefficient (NSE) values of 0.49 and 0.955 were achieved, respectively, for current threshold conditions. Durations of temperature increases from threshold levels indicate that land use changes from current agriculture conditions to urbanization may change stream water temperatures for 9% of the time by 1 °C, and 2% of the time by 2 °C for distances of 1000 m downstream, because of land use change from agriculture to low-density urbanization, and for 20% of the time by 1 °C, and 4% of the time by 2 °C at distances of 1000 m downstream with land use change to high-density urbanization. With climate change RCP 4.5 Scenario in 2050 (Base, for a Wet Year—2017), the continuous amount of time the stream water temperature remains at elevated temperatures of more than 3 °C (from 5000 m to 25,607 m from the most upstream point of Fletchers Creek) for a distance of 20,000 m is more than 13 h. These elevations in temperature may have serious implications for flora and fauna in the creek, particularly impacting the cold-water and mixed-water fish species.

Cyanobacteria, also known as blue-green algae, are photosynthetic bacteria that play a crucial role in aquatic ecosystems and are susceptible to changes in temperature. Hence, as global temperatures rise due to climate change, some Cyanobacterial species will thrive in warmer temperatures, which will result in increased blooms during the growing season. The MIKE-3 model is calibrated to existing (2022) conditions and is used to assess the impact of the RCP 4.5 scenario for the year 2050 in Fairy Lake (a shallow urban lake in Ontario). The simulations projected indicate that in 2050, in the central parts of Fairy Lake’s central basin, water temperatures will be above 20 °C for 2281 h compared to 2060 h in 2022. This situation indicates there will be a 10.7% increase in the duration of Cyanobacteria blooms in the central area of Fairy Lake. Similarly, in the northern area of Fairy Lake, the MIKE-3 model results indicate that surface temperature durations above 20 °C will increase from 1628 h to 2275 h for the year 2050, resulting in an additional 647 h of increased temperatures at the surface under RCP 4.5 scenario conditions. This situation indicates there will be a 39.7% increase in the duration of Cyanobacteria blooms in the northern portion of Fairy Lake. These modeling conditions indicate there will be significantly more habitat amenable to Cyanobacteria growth when surface water temperatures are above 20 °C, indicating substantial increases in the available growth time of Cyanobacteria due to climate change, all of which translate to major concerns caused by climate change.

Cyanobacterial harmful algal blooms (cHABs) pose increasing ecological and public health risks in shallow lakes subject to nutrient enrichment and climate change. This research describes and evaluates a three-dimensional hydrodynamic ecological modeling framework for Fairy Lake, Ontario, using MIKE 3 FM coupled with ECO Lab to simulate lake circulation, thermal structure, nutrient dynamics, and cyanobacteria (PC3) concentrations, with model calibration using 2022 data observations and validation using 2023 data. Hydrodynamic performance showed moderate agreement for lake levels (NSE 0.47–0.52) and strong predictive capability for water temperature (NSE up to 0.96 across depths). Nutrient simulations reproduced seasonal nitrate and phosphate trends, with sediment parameter adjustments to stabilize internal loading dynamics. Cyanobacteria simulations captured seasonal bloom timing and spatial variability between inflow and central basin zones during the calibration and validation periods. The results demonstrate that integrated 3D hydrodynamic ecological modeling reproduces seasonal bloom dynamics in shallow polymictic lakes employing calibrated models and subsequent data, to predict sediment nutrient processes and periodic reassessments. As a result, this framework provides a quantitative basis for evaluating bloom behavior and the ability to predict management scenarios able to test changing climatic and nutrient conditions.

Large numbers of urban lakes are facing issues related to cyanobacteria, commonly known as blue-green algae, resulting in significant threats to humans and animal health due to their production of microtoxins and Anatoxin-A. These toxins induce acute effects including gastrointestinal distress, and respiratory problems, underscoring the need to protect urban lakes to safeguard community health and ecosystem well-being. A comprehensive monitoring program is a critical step to address cyanobacteria-related issues. Monitoring results of dissolved phosphorous, nitrates(N), Total Kjeldahl Nitrogen (TKN), total phosphorous (TP), TSS, and Escherichia coli (E. coli) concentrations, are used to understand the importance of different pathways events during dry conditions (no prior rainfall) and wet events (rainfall during or proceeding monitoring events) plus a microbial source tracking procedure, to understand impacts on growth characteristics of cyanobacteria and microtoxins. The Mann-Kendall Trend Test is used to characterize trends of various parameters (using transitions of ‘wet’ and ‘dry’ to the Lake and within the Lake), to identify the impact of various management strategies and/or the impact of various sources from overland land uses for a) wet events to the Lake, b) dry events to the Lake, c) wet events in the Lake, and d) dry events within the Lake. Microbial source tracking methods are used along the shoreline of Fairy Lake to interpret elevated levels of fecal pollution and E. coli bacteria in water samples, aiding in the identification of pollution sources. Blue-green algae have been observed at least once each year from 2018 to 2023. Microtoxins and Anatoxin-A were present in nine samples with a maximum of 1.72 mg/L and 0.02 mg/L, respectively. Frequent beach closures have occurred every year, raising public concerns regarding both ecological and recreational aspects for Fairy Lake.