The main paths of some pesticides and their levels in the trophic compartments of the benthic food web of the Mar Menor, an oligotrophic coastal lagoon located in the SE of Spain, are studied in this paper. A total of 78 samples of water, sediment and benthic organisms were analysed. The analytical determination of organochlorine and organophosphorus insecticides was realized through gas–liquid chromatography with specific detectors (ECD and NPD, respectively). For triazine herbicides determination we used inmunoenzymatic technique. Residues of organochlorine insecticides and/or any of their analysed metabolites were detected in 70.5% of the controlled samples, though at small concentrations. In any case, residues of organophosphorus insecticides were detected and only traces of triazine herbicides were found in sediments (0.1–1 ng g⁻¹). Between the detected compounds stand out the presence of endosulfan in 51.3% of the analysed samples followed by HCH (47.4%) and endrin (18%). The highest concentrations are reached in organisms (in the green algae Chaetomorpha linum and in the isopod Idotea basteri, with 1475 and 603 ng g⁻¹ of endrin, respectively) followed by sediments (662 ng g⁻¹ of endosulfan) and water (13 μg l⁻¹ of endosulfan). Inputs of pesticides into the trophic web take place mainly through plants to the herbivorous–detritivorous compartment. The maximum bioconcentration factor is shown by the gammarids for heptachlor compounds (30980 times the concentrations in water).