Estuarine species exposed to diffuse contaminants might trigger either positive or negative feedbacks in many biological scales. Their life history traits performing at different biological organization levels could propose an organism as a useful indicator of environmental pollution, mainly addressed as sensitive or tolerant species. To track the effects of contaminants from the molecular to the population level of the polychaete Laeonereis acuta we utilize a framework of biomarkers. For this purpose we assessed the L. acuta frequency of micronuclei at the molecular level, the body size and biomass at individual level, and the production-to-biomass ratio at population level in five urbanized and five non-urbanized estuaries in southern Brazil. L. acuta had significantly varying positive and negative feedbacks between urbanized and non-urbanized estuaries at multiple biological scales. These generalized effects in all biological organization scales indicate a pollution impact on the polychaete. The main responses accounted for individuals becoming lengthy and weighty, but with molecular damage. The L. acuta allocation of energy to body enlargement in polluted environments, and a consequent reduced population turnover, contradicts the expected from an opportunist species. The damages in DNA and the internal strategies of individuals, as antioxidant defense mechanisms, could favor resistance of the population and tolerance to pollutants. All of these characteristics induce bioaccumulation and could cause bottom-up pollution transfer compromising the estuarine food web. These results, ascertain that L. acuta could be considered as a tolerant species, instead of an opportunistic, and as a useful indicator of environmental pollution in estuaries