This study uses the local knowledge of artisanal fishers to assess ecosystem structure, functioning, and fishing impacts within a coastal lagoon in Uruguay. To this end, we used an Ecopath with Ecosim modelling approach based on fishers’ knowledge and scientific data. The model considered 23 functional groups, while three fleets represented fishing activities targeting different species. The model output shows a foodweb which spans four trophic levels, including fish species as top predators, such as the flatfish Paralichthys orbignyanus and the tararira Hoplias malabaricus. Furthermore, according to fishers’ knowledge, gastropods, polychaetes, and bivalves constitute primary consumers, while detritus and phytoplankton represent the primary food sources. The trophic impact analysis shows that the fish Mugil spp. and Odontesthes spp. generate important positive and negative impacts on most other ecosystem components, while fishing impacts occur at moderate exploitation levels on the targeted fish species. The indicators of the ecosystem effects of fishing including The Trophic Level of the Catch ranging from 2.4 to 2.6, the Primary Production Required showing relative low values of 2.3% and low probability of an ecosystem being sustainably fished alert us to the risk of ecosystem-level overfishing. The vast potential of fishers’ knowledge in research can allow the co-creation of new insights into ecosystem structure and function. By including fishers in research, local communities can be empowered and benefit from management decisions through their trust in science.