Organic enrichment, especially from anthropogenic sources, is one of the current threats to coastal marine biodiversity. Organic enrichment occurs mainly in sheltered soft bottoms, characterized by fine sediments, and results in multiple changes in the benthic habitat, including hypoxia and an increased concentration of compounds that are toxic to marine invertebrates. We report on the results of a microcosm-based experiment (duration = 30 d), quantifying the effects of organic enrichment on taxonomic and functional diversity of nematode assemblages from an open/closed coastal lagoon of South America (Rocha Lagoon, Uruguay). In open/closed lagoons, the input of organic matter becomes a major disturbance due the limitation in water renewal. In our experiment, enrichment led to reductions in abundance, richness and trophic diversity of the nematode assemblage. Rapid reductions in total abundance (after 4 d) were registered, while richness decreased only towards the end of the experiment (~30 d). Trophic changes were characterized by loss of predators/omnivores and dominance of selective deposit-feeders and epigrowth-feeders. By contrast, we did not find any selective effect of enrichment associated with life history traits (e.g. maturity index). Overall, these findings have 2 important implications for the conservation and monitoring of the health of coastal lagoons: first, monitoring of nematode assemblages at the genus level is sufficient to detect enrichment effects; second, an index of trophic diversity would be a good indicator of the effects of enrichment on natural communities.