The Jundiaí-Mirim watershed supplies the Jundiaí city and it is located between two metropolitan regions: the Campinas metropolitan region and the São Paulo metropolitan region which are the two most populous regions in São Paulo state. In this region some problems such as hydric resources scarcity, as well the water quality; conflicts between the water users and hydric pollution are part of the reality faced by the management agencies and government. The trophic state index (TSI) allows the water bodies classification according to the nutrients entrance into the system. That contribution artificially stimulates the algae and macrophytes proliferation and may causes a number of problems which includes: toxic algae proliferation, fish kills and disagreeable odor. The benthic macroinvertebrates are one of the most widely and recognized bioindicators in the aquatic environments reacting to impacts in water column, sediment and margins. The objective of the present research was to assess the environmental quality of the Jundiaí Mirim basin based on the trophic state index and the benthic macroinvertebrates community. Samplings were performed for TSI calculation and benthic macroinvertebrates rapid analysis at four samplings stations along the Jundiaí-Mirim river basin (Jundiaí, SP, Brazil). The data obtained reveals a worrying situation of the basin which is suffering a eutrophication process resulting in a poor quality of its waters and sediments. Moreover, it was recorded the presence of the exotic mollusk Corbicula fluminea, one of the freshwater exotic species of main concern in the world. It is recommended the development of an action project comprising short, average and long term marks in order to promote the recovery of the environment and to avoid environmental, social and economic problems. A rapid analysis index using the benthic macroinvertebrates was proposed.