The Estero de Urías coastal lagoon is subjected to several anthropogenic activities and has been characterized since 1997 through the study of benthic fauna. We analyzed the spatial and temporal distribution of annelids and their relationships with environmental variables (depth, sediment temperature, grain size and organic matter) in order to determine the current degree of perturbation. Density, species richness, diversity, dominance, biomass, and the application of classification and ordination techniques allowed us to distinguish 5 zones: 1) a non-perturbed zone at the mouth of the lagoon, 2) a slightly perturbed zone surrounded by mangroves and shrimp farms, 3) a temporarily perturbed zone close to the effluent of the thermoelectric plant, 4) a perturbed zone in front of the slaughterhouse and fish factory, and 5) a very perturbed zone subjected to sewage and industrial input. Only minor changes in granulometry and faunal composition were observed in comparison with previous data from the same area, suggesting that the lagoon is still perturbed due to the effect of anthropogenic activities.