Contaminants of emerging concern (CECs) have not been extensively studied in Caribbean estuaries, particularly in Puerto Rico. Polar organic chemical integrative samplers were deployed in surface waters at five sampling sites in the San Juan Bay Estuary to investigate the occurrence and distribution of 137 CECs, resulting in the detection of 64 chemicals (51 pharmaceuticals and personal care products "PPCPs", 12 hormones plus sucralose) at least in one sampling site, and with 35 chemicals obtaining a 100 % detection frequency. Wastewater intrusion was implicated in the presence of CECs based on the detection of sucralose and other wastewater tracers. Condado Lagoon was the most polluted site impacted by untreated wastewater, showing the highest levels of 30 of the 64 detected CECs, and the largest proportion of detected CECs, particularly PPCPs. Levels of estrone and 17β-estradiol represent a high potential risk for adverse effects on aquatic organisms in this Caribbean urban estuary.