This study focuses on modeling water quality in mangroves areas including the effects of wetting and drying processes on the biogeochemistry of the mangrove. To achieve it, we use a shallow water hydrodynamics model capable of predicting both water quality and wetting and drying, which uses a rough-porous layer approach based on the water level. To evaluate the capabilities of the model, we consider an estuary region in Brazil to evaluate the model's capabilities. The simulations carried out show the hydrodynamic behaviors and effects related to the water quality parameters in a complex tidal system comprised of extensive mangrove flats.