Sedimentation in estuaries and coastal seas is an important concern due to the rapid morphological changes induced in the coastal zone. When the sediments coming from the continent are important, this problem is increased because they introduce morphological consequences, but also, they can transport several kinds of organic and inorganic pollutants due to anthropogenic activities in the hydrological basin. In this fact sediments play an important role with the consequently drop of the water quality in the environment. In this paper, the hydrodynamics is solved with a multilayer approximation and afterwards coupled with the resolution of total load of sediments (composed by suspended, bed and transition layer). Hydrodynamics calculation take into account tidal flow, wind driven influences, mass balance between fresh and salt water, and the hydrological influence on the river. Horizontal plane is considered with either a homogeneous or non-homogeneous grid; in the vertical, the model considers a numerical integration by layers.