Growth of the aquaculture industry has triggered the need for research into the potential environmental impact of chemicals used by salmon farms to control diseases. In this study, the antiparasitic pesticides emamectin benzoate (EB), diflubenzuron (DI), teflubenzuron (TE), and cypermethrin (CP) were measured in sediments near salmon cages in southern Chile. Concentrations for EB were between 2.2 and 14.6ngg−1, while the benzoylphenyl ureas DI and TE were detected in the ranges of 0.1 to 1.2ngg−1 and 0.8 to 123.3ngg−1, respectively. These results were similar to data reported for the Northern Hemisphere. On the other hand, the pyrethroid CP was detected in higher concentrations, ranging from 18.0 to 1323.7ngg−1. According to reported toxicity data, this range represents a potential risk for benthic invertebrates. This report is the first baseline attempt at assessing antiparasitic pesticide levels in the Chilean Patagonia.