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Little is known about the presence and effects of polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs) in Puerto Rico’s waters. Four coastal aquatic systems were investigated using low-density polyethylene passive sampling for PCBs and OCPs in water and its overlying air. The highest total freely dissolved and gaseous concentrations of PCBs were found in Guánica Bay, with 4000 pg/L and 270 pg/m3, respectively. Five OCPs were detected, mainly in water, with greatest concentrations (pg/L) in Guánica Bay: α-HCH (7400), p,pʹ-DDE (390), aldrin (2000), dieldrin (420), and endrin (77). The compound α-HCH was also measured at elevated water concentrations in Condado Lagoon (5700 pg/L) and Laguna Grande (2900 pg/L). Jobos Bay did not show values of concern for these persistence organic pollutants. Levels of PCBs and OCPs in water, particularly in Guánica Bay, exceeded USEPA ambient water quality criteria values representing a human health risk regarding consumption of aquatic organisms.