Algal fouling has become a serious problem along Great Lakes' coastlines and difficult to diagnose due to spatial and hydrodynamic variability typical of nearshore zones. We applied a three-dimensional hydrodynamic-ecological model to a coastal segment of Lake Ontario to provide insight into the role of dynamics and external inputs relevant to algae growth. Lake-wide simulations with a 2 km grid were coupled to a higher resolution (100 m grid) domain. The nearshore model captured the complexity of stratification, mixing and upwelling, while revealing circulation patterns not evident at the lake-wide scale, likely exacerbating the local fouling problems. A wastewater outfall produced peaks in the spatial dynamics of TP and SRP in the nearshore, which decayed by 80% within the first kilometer of the outfall, and introduced considerable variability in P distributions. Tributaries affected TP distributions during high runoff periods but had smaller effects on SRP. Seasonal dynamics and average values of chlorophyll a in the domain were well reproduced, but there was evidence for an unrecognized sink for nitrate and/or errors in estimated nitrate loads. Comparisons between a dry year (2007) and wet one (2008) revealed only limited immediate effects on water quality variables from local tributary discharges. The model was able to predict major water quality variables that are important to nuisance algae growth despite present exclusion of dreissenid mussels and associated nutrient cycling. Simulations predicted repeated brief episodes of relatively high SRP, hard to capture in most observational programs but, if verified, would have important implications for nuisance algae growth.