Shrimp farm aquaculture causes environmental impacts, notably decreased water quality due to the release of nutrient-rich effluents. Pond wastewater is usually discharged without treatment, and tidal conditions are not taken into account in the management plans. However, natural variability of nutrients makes difficult field evaluation and attribution of impacts. Here we implemented a three-dimensional coupled hydrodynamic-biogeochemical model (spatial resolution = 50 m × 50 m, time resolution = 4 s) in order to evaluate the dispersion conditions under specific tidal conditions of nutrient discharges from a semi-intensive shrimp farm during spring and neap tide. Ammonia was quickly assimilated by plankton and its concentration recovered initial levels 10 days after the beginning of the harvest. Due to the higher salinity of the pond effluents, shrimp farm discharges accumulate in waters and sediments of the upper lagoon creeks, mostly affecting the benthos, thus implying a potential risk of shrimp farm self-contamination. Maximum concentrations of most biogeochemical tracers occurred when the harvest ends and the ponds are fully emptied. We show that maximum nutrient concentrations can be reduced by ~ 10% when the harvest ends during spring tides compared to harvests ending during neap tides. This work may be useful to improve the management of shrimp farm effluents by reducing, easily and at little cost, nutrient impacts on tropical and sub-tropical receiving ecosystems.