As of today the Virrilá Estuary located in Piura, Peru, is polluted with high nitrate and chlorine concentrations. Because of that the mariculture activity of the towns and cities located in that estuary are significantly affected (which is the basis of their economy). Recent field measurements indicate that the nitrate concentrations are related to the suspended sediment concentrations whereas the chlorine distribution is directly associated with the flow recirculation patterns. In order to shed light on the transport dynamics of these contaminants a two-dimensional shallow water equations numerical model that can predict suspended sediment transport and flow recirculation was developed. Field data measurements were used as input to the numerical model and comprised the pollutants concentration, tides data, wind speed and direction, suspended sediment concentration, inflow discharges, and bathymetry. The results of the numerical model showed that the flow patterns of the estuary are mainly driven by the variation on water levels alone and that the interaction of suspended sediment concentrations occurs only in areas near the mouth of the Virrilá Estuary. © 2018 American Society of Civil Engineers.