Stable isotopes ratios (delta C-13 and delta N-15) were measured in primary producers and consumers of two bays with contrasting eutrophic conditions in the pains Lagoon estuary, southern Brazil: the Justino bay, a more pristine ecosystem, and the Mangueira bay, a heavily polluted region that receives the Rio Grande city sewage and effluents of several industries. delta C-13 values of organisms collected in both subsystems were not different, but delta N-15 values had significant statistical differences, ca. 3.5 parts per thousand higher in the Mangueira bay. It is likely that primary producers and consumers in this subsystem are greatly influenced by higher nitrogen input due to domestic and industrial sewages. The stable isotope analysis also corroborated several trophic interactions previously established by gut content analysis, and due to its higher sensitivity, it was possible to better determine the contributions of different primary producers and detrital fractions to the consumers' diets. It was confirmed that plant detritus represents the main food source for most organisms. The stable isotope analysis also demonstrated that detritivorous benthic organisms in the same habitat have distinct diet compositions, with differential consumption of C3 and C4 plants. This technique showed that some consumers that eat detritus do not have in their stable isotopic signature any relationship with that of plants. It is likely that these consumers assimilate their carbon and nitrogen from other sources like microalgae or microorganisms that colonize decaying plants.