Torrecilla Lagoon, part of the San Juan Bay Estuary system, is a moderately-polluted estuary on the northern coast of Puerto Rico. Foraminiferal assemblages from two 30 cm cores were dominated by Ammonia spp. and Quinqueloculina rhodiensis. The latter taxon exhibits a relatively high occurrence of deformed tests (up to 18%). Analyses for potentially toxic-element in bulk sediment samples of one core show concentrations below recognized toxicity levels except for copper. Copper concentrations (50–138 ppm) fall between previously established Effect Range Low and Effect Range Median values, representing potential for occasional detrimental effects to the aquatic environment. Organic matter content (loss-on-ignition) ranging from 10–23%, coupled with the presence of framboidal pyrite, indicate low oxygen conditions. Ammonia spp. showed no significant variation in size with depth in core. Ammonia-Elphidium index values, a previously established indicator of hypoxia, are 69–100, reflecting relative few Elphidium. Species diversity indices indicate temporal variability in abundance and distribution of foraminifers. Foraminiferal assemblages and organic matter in sediments indicate that Torrecilla Lagoon has undergone episodes of hypoxia.