A detailed investigation on the contamination with chlorinated hydrocarbons and organophosphorous pesticides of the coastal lagoon system of Chinandega district, Nicaragua, allowed the identification of contaminant sources and lagoon areas currently more contaminated. The discharge of rivers into the lagoons is the main transport pathway of pesticide residues; whereas atmospheric depositions are likely to be the main pathway for the introduction of PCBs into the lagoons. Analysis of water samples indicates widespread contamination with soluble organophosphorous compounds, such as dichlorvos, up to 410 ng L⁻¹, diazinon, up to 150 ng L⁻¹, and chlorpyrifos, up to 83 ng L⁻¹. Analyses of suspended matter for low solubility organochlorine (OC) compounds revealed very high concentrations of toxaphene, up to 17450 ng g⁻¹ dry weight (dw), total DDTs up to 478 ng g⁻¹, Aroclor 1254, up to 119 ng g⁻¹ (dw), and lower concentrations for other compounds. Lagoon sediments contain high concentrations also of toxaphene, from 7.9 to 6900 ng g⁻¹ (dw), and DDTs, from 1.5 to 321 ng g⁻¹ (dw), and lower concentrations of chlorpyrifos, hexachlorocyclohexanes, chlordane and other residues. Concentrations of OCs in soft tissues of clams are statistically correlated with the concentrations of the same compounds in bottom sediments, indicating that sediments are a source of contaminants to biota. In some areas of the lagoon system, concentration of residues in sediments are far above recommended threshold guideline values for protection of aquatic life, and may cause acute and chronic toxic effects on more sensitive aquatic species. Despite the ban on the use of toxaphene and DDT, residues of these compounds are still entering the lagoons due to erosion of, and leaching from, agriculture soils in the region. Measures for protection of the lagoon ecosystem are discussed.