The growth of human populations and industrial activities in the last decades have been the major cause of ecosystem decline, especially due to the inputs of several pollutants in the environment. Estuaries are one of the main concerns in marine governance because they receive potentially toxic substances from many sources that end up in the sea. Despite this, marine policies that aim to protect marine areas have dismissed local fishers' knowledge, although fishers have ecological knowledge that endorses and complements scientific research. Therefore, the aim of this study was to identify sources and indicators of pollution in the Bahía Blanca Estuary (BBE) according to the fishers and to contrast this knowledge with scientific studies. We conducted 20 interviews with the fishers of the BBE, and the results showed that all of them think the estuary is polluted and that there have been changes in the biomass of catches in the past. Most of them think that industries of the petrochemical complex are the major cause of pollution (57%), while marine organisms were the most mentioned items as indicators of pollution (59%), especially the commercial species (41%). We found interesting parallels between fishers' ecological knowledge (FEK) and scientific data. Thus, we conclude that FEK is an invaluable tool that provides data that could help to co-protect and co-manage this estuary and the services it provides.