Environmental modeling has been an indispensable tool of the Hamilton Harbour restoration efforts, where a variety of data-oriented and process-based models have been used for linking management actions with potential ecosystem responses. In this study, our objective is to develop a biogeochemical model that can effectively describe the interplay among the different ecological mechanisms modulating the eutrophication problems in Hamilton Harbour, Ontario, Canada. First, we provide the rationale for the model structure adopted, the simplifications included, and the formulations used during the development phase of the model. We then present the results of a calibration exercise and examine the ability of the model to sufficiently reproduce the average observed patterns along with the major cause—effect relationships underlying the Harbour water quality conditions. The present modeling study also undertakes an estimation of the critical nutrient loads in the Harbour based on acceptable probabilities of compliance with different water quality criteria (e.g., chlorophyll a, total phosphorus). Our model suggests that the water quality goals for TP (17 µg L^-1) and chlorophyll a concentrations (5–10µg L^-1) will likely be met, if the Hamilton Harbour RAP phosphorus loading target at the level of 142 kg day^-1 is achieved. We also provide evidence that the anticipated structural shifts of the Zooplankton community will determine the restoration rate as well as the stability of the new trophic state in the Harbour.