This work is part of the Treatment/remediation and recovery of bays project using innovative procedures project led by CITBM and funded by the National Science, Technology and Technological Innovation Council (CONCYTEC in spanish) through the program CIENCIACTIVA. Thanks to Water Research Center CITA-UTEC for the support with the instrumentation for the measurements campaign; Tobias Bleninger and Julio Werner for background and feedback, Carlos Landauro, Justiniano Quispe and César Aguirre for the administrative and logistical support in the measurements. Thanks to Hugo Montoro, Tania Rojas, Mishel Meléndez, and Sofía Valdivia for the support with information processing. Thanks to Herver Caruzo, Elivorio Castillo for the support in the measurements and the transportation of equipment

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.