Organic enrichment is a major threat to coastal environments, yet its impact on meiobenthic animals remains poorly understood. In marine sediments, copepods belong to the dominant taxa and they are known to regulate organic matter degradation and nutrient cycling. Here we performed a large-scale observational study to assess the impact of an increase in organic matter on meiobenthic copepod. We established a relation between the content of organic matter that reaches the coasts through eight rivers and the richness and diversity of meiobenthic copepods. In each site, three sampling points were considered (river-mouth, 200 m north, and 200 m south) and for each of these we estimated taxa diversity and taxa richness, organic matter concentration, and environmental parameters. We found that organic enrichment was negatively correlated with both taxa diversity and taxa richness, and this relation was stronger at river mouths. We also found a synergic interaction between salinity and organic matter content; instead, temperature and pH seemed not to be structuring the copepod community. This study provides evidence of the potential negative impact of coastal organic enrichment on the copepod diversity.