In this study we focused on the freshwater zone of the estuary, where we observed an overlap on the distribution of species that responds to natural factors and anthropogenic stress, and noticed that with the deterioration of water quality, as a result of increased anthropogenic pressure and the input of organic matter and nutrients, some phytoplanktonic species increased their proportion in the assemblage. We recognized that 24 species, common in the coastal phytoplankton of the freshwater zone of the estuary (Gómez and Bauer, 1997; Gómez and Bauer, 1998; Gómez et al., 2002; Gómez et al., 2004; Gómez, 2014; Sathicq et al., 2014), were able to thrive under such conditions. The percentage of this group of tolerant species allowed us to have an indicator capable of detecting the impairment of the water quality in different sites of the study area.