Water quality degradation, in the form of undesirable algae, occurs near the Nottawasaga River mouth and along Wasaga Beach, located in southeastern Georgian Bay, Ontario. Runoff from fertilized agricultural areas, in the Nottawasaga River basin, is major source of nutrients (phosphorus (P) and nitrogen (N)) entering Nottawasaga Bay through the river, which stimulate the growth of excessive phytoplankton along Wasaga Beach. Coupled three-dimensional hydrodynamic and ecological models ELCOM – CAEDYM (ELCD) were applied to investigate (i) the advection and dispersion of a passive tracer, flowing from the Nottawasaga River, to examine the physical processes that can trap nutrients along Wasaga Beach and (ii) the difference, in model results, between using literature and observed values for P fractions and phytoplankton community distributions in Nottawasaga Bay. Model hydrodynamics were comprehensively validated against temperature and current profiles collected during May-September, 2015, with root-mean-square errors (RMSE) between 1.5 oC to 2.5 oC and ~0.06 m/s, respectively. For an average river discharge rate of 17.6 m3/s, the tracer concentration and occurrence were dominated either by wind speeds >2 m/s or by river discharge for wind speeds < 2 m/s. Hydrodynamics also controlled the distribution of total chlorophyll-a (TChl-a) in Nottawasaga Bay. After model initialization, the initial condition predominated, until an upwelling event in northern Nottawasaga Bay propagated along Wasaga Beach. This caused a sudden drop in the simulated TChl-a and the model to reset from the lake initial conditions. Thereafter, Nottawasaga River inputs, trapped nearshore, regulated Wasaga Beach water quality. The simulations did not show much discrepancy between using constant literature and observed values for phytoplankton community initial and boundary conditions in Nottawasaga Bay, where calculated RMSE were ~1.2 g chl-a/L. However, there was a noticeable influence in including particulate inorganic P as a measured P fraction on simulated TChl-a (RMSE = 1.06 mg chl-a/L). Neglecting PIP in the total P budget, as is commonly done in model applications, resulted in all particulate organic P (POP), from the Nottawasaga River, being available for uptake by phytoplankton, causing spurious algal growth in the P limited system.