Surface sediments from Reloncaví Fjord and the Chiloé inner sea in Chilean Patagonia were extracted and analyzed to estimate deltamethrin and diflubenzuron levels. These antiparasitary pesticides have been used for decades in the salmon industry. Relationships were determined between pesticide concentrations and organic carbon percent in sediments. Deltamethrin (0.39–1.05 µg g−1 dw) was found at all sampling sites but diflubenzuron (0.06–0.09 µg g−1 dw) at only five. Diflubenzuron levels were similar for sediments from other fjord areas. However, deltamethrin concentration was 2–3 fold higher than other studies on this area. The organic carbon percent was correlated positively and significantly with diflubenzuron, but not with deltamethrin. Our results suggest that the high deltamethrin concentrations in sediments are due to the increased use of pyrethroids around salmon farming areas. But, the diflubenzuron levels can be explained by degradation processes.