This paper investigates the seasonal evolution of the spatial distributions of dissolved inorganic nitrogen and phosphorus, in relation to the estimation of the N and P loads, which were obtained in the framework of the DRAIN project. Such investigation is carried out by using a 3D reaction-diffusion model which has been calibrated against salinity data and then used for obtaining the most likely scenario of the spatial and seasonal distribution of DIN and DIP. The consequences of different management policies are also discussed, in relation to the current Italian legislation, which sets quality standards for both DIN and DIP in the lagoon of Venice.