This paper describes the ecohydrodynamic predictive model EcoPuckBay—the ecosystem part—for assessing the state of the Puck Bay coastal environment and its ecosystem. We coupled the EcoPuckBay model with the land water flow models (Soil and Water Assessment Tool (SWAT) for surface water and Modflow for groundwater). To evaluate the quality of the results obtained from the EcoPuckBay model, a set of basic statistical measures for dissolved oxygen, chlorophyll-a, nitrates, and phosphates were calculated, such as mean, Pearson correlation coefficient (r), root-mean-square-error (RMSE), and standard deviation (STD). The analysis presented in this paper shows that the EcoPuckBay model produces reliable results. In addition, we developed a nutrient spread module to show the impact of agricultural activity on the waters of the Puck Bay. The EcoPuckBay model is also available in operational mode where users can access 60-h forecasts via the website of the WaterPUCK Project through the “Products” tab.