This study provides baseline information on the extent of contamination in sediments of the Jobos Bay estuary and surrounding areas in Puerto Rico. Sediments from Jobos Bay area (n = 14) had higher overall average concentrations than those from La Parguera area (n = 5, used as reference site), in μg/g dw, for As (17 vs 9), Cu (29 vs 14), Pb (11 vs 4), and Zn (64 vs 28); and in %, for Fe (2.6 vs 0.6). Sediments (n = 8) screened for PAHs and PCBs exhibited total concentrations (ng/g dw) that ranged from 40.4 to 1912, and from not detected to 11.21, respectively. The quality of sediments of Jobos Bay could be classified as low to moderate pollution. The proximity to anthropogenic sources of contamination warrants a monitoring program for inorganic and organic pollutants in Jobos Bay area for an effective coastal management program of this tropical ecosystem.