Assessing the ecological quality status of a temperate urban estuary by means of benthic biotic indices

•Performance of ecological indices was tested for the Montevideo coast.•An impoverishment in the environmental quality was shown.•AMBI with a set of variables appeared to be suitable to assess environmental quality.•The condition probability allowed defining new threshold of impairment on biota. Benthic indices are commonly used tools for assessing the environmental quality, because they represent a simple source of scientific information. However, their performance could vary depending on the application area and perturbation types, thus they should be tested before used in other remote geographic regions. This study aims to test the use of some of the most widely common benthic biotic indices for assessing the environmental quality of Montevideo’s coastal zone at a seasonal scale against many physicochemical variables. From all the evaluated indices, AMBI appears to be the most suitable one to assess the environmental quality. The study also allowed us to infer the most relevant physicochemical variables: protein, lipid and heavy metal sediment concentration. Additionally, site-specific threshold effect levels for heavy metals and biopolymers were established, which appear to be useful to determine tolerable levels of such stressors in future assessments or monitoring programs for the study area.