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.