Analyses of pesticide residues in sediments, water and biota of the Altata - Ensenada del Pabellon coastal lagoon system in Sinaloa, Mexico, showed the presence of organochlorine and organophosphorus compounds. For all the compounds analysed, concentrations in sediments were higher near the points of water discharge from ponds and drainage from the agricultural area. Among the organochlorines, total DDTs displayed the largest sedimentary reservoir, followed by total endosulfans and chlorpyrifos. In sediments, as well as in biota, pp′-DDT concentrations were lower than those of DDT metabolites, which confirms the reduction in the previous massive use of this compound in agriculture. Endosulfan is currently used in the region and endosulfan residues in lagoon sediments attained levels considered to be toxic to meiofauna, therefore constituting an ecological risk to lagoon ecosystems. There was a large sedimentary reservoir of chlorpyrifos but its ecotoxicological risk is difficult to assess due to lack of adequate comparative data. Nevertheless, concentrations of chlorpyrifos which approach acute toxic levels for shrimp were recorded in lagoon water. This suggests that drainage from agricultural fields during high runoff may, on occasion, cause mass mortality of shrimp and fish. Organophosphorus pesticides are widely regarded to degrade very rapidly in aquatic systems. Experimental research performed with 14C-labelled chlorpyrifos and parathion has shown that they may be stabilised for relatively long periods of time through sediment-water partitioning. This extension of their environmental half-lives increases their potential for impacting on coastal ecosystems. Since organophosphorus pesticides are highly toxic for aquatic organisms at concentrations generally lower than organochlorines, their presence in the lagoon water and sediment is a matter for much concern. The increased use of tropical coastal lagoons for shrimp and fish farming requires the implementation of environmental management practices to protect these ecosystems from the impact of agricultural activities. Environmental management aims to preserve the ecosystem integrity of these coastal lagoons and, through improving the water quality, to allow the development of aquaculture and reduce human exposure to pesticide residues in food.