The Jobos Bay National Estuary Research Reserve (JBNERR) in Salinas, Puerto Rico, has served as sink for many anthropogenic substances that may affect the quality of the soil and water and the integrity of the biota. Four transects were established in the southeastern part of JBNERR for interstitial water collection. In addition, soil samples were collected from transects I, II, and III, at sites that were affected by runoff from a road closer to the Salinas landfill. The concentration of lead (Pb) in interstitial water from the above mentioned transects ranged from 0.07 to 0.68 mg/L: chromium (Cr) concentration ranged from 0.03 to 0.24 mg/L; and manganese (Mn) concentration ranged from 0.35 to 15.25 mg/L. The total Pb in soil samples ranged from 59 to 758 mg/kg, in an uneven distribution along transect II. The low Pb concentrations in water in comparison to that in soil indicate the high capacity of the JBNERR soils to serve as sink for heavy metals. The linear correlation between Pb concentrations in the interstitial water and the electrical conductivity suggests that marine water increases Pb remobilization from soils. Also detected in interstitial water were anthropogenic organic compounds such as benzothiazole, 1-methyl-2- pyrrolidinone and tert-butyl phenol; however, no residues of pesticides used from agricultural farms nearby were found. Results have shown that human activities have affected soil and water quality in the JBNERR.