The marginal lagoons of the Sorocaba River fulfil important functions in their lotic ecosystems and for its fish communities, providing shelter, food, and area for fish early stages of development. The lagoons are also an escape from the river pollution since the physical-chemical characteristics of their water are more stable than the river water. Nevertheless, these lagoons are under a series of impacts that contribute to reduce their diversity and stability such as water pollution, deforesting and river dumping. These impacts decrease habitat availability, and modify the fish community structure by reducing the number of species in the Sorocaba River, the floodplains and its marginal lagoons.