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The environmental quality of mangroves is influenced by multiple factors, among which shrimp aquaculture currently plays a major role. This study describes the alterations of natural conditions of mangrove systems that house shrimp farms in the northern Ecuadorean coast. Water, sediment quality and the structure of benthic assemblages of four sectors with different proportions of mangroves and shrimp ponds are described. The samples were collected at the confluence of mangrove drainages or tidal creeks, as well as in the modified drainages for shrimp farm infrastructures towards navigable channels, during the dry and rainy seasons. Shrimp farm drainage water had a 17% higher dissolved oxygen concentration and 2.5 times higher total ammonium and phosphorus compared to mangrove drainage water. The sediment in the latter decreased their total organic matter and nitrogen content by 44% and 53%, respectively, slightly increasing the pH level and increasing the ammonium content by 93%. Furthermore, the redox profiles were different between the types of drainages. The soft-bottom benthic assemblages involved 56 species in the study area and exhibited a variety of sectoral structures, with better indicators of ecological status in sectors with fewer shrimp farms. Finally, improvements are suggested for monitoring the environmental quality of shrimp farms in Ecuadorean mangrove systems.