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Urban runoff was one of the leading sources of water pollution of particular concern at Ciénaga Las Cucharillas Watershed (CCW), an urban coastal watershed in northern Puerto Rico with a high density of industrial and residential activities. Research was conducted to characterize the possible relationship between land use land cover (LULC) change patterns, and the current toxic metals (TMs) content in aquatic sediments of Canal La Malaria (CM), Ciénaga Las Cucharillas Watershed (CCW) drainage waterway. The watershed has been modified from its natural conformation, hydrologically connected to the San Juan Bay, to a canalized one. The uncertainty of the potential outcomes resulting from the disposition of anthropogenic wastewaters in the area was a major environmental management issue. There is scarce information on the geoavailability of TMs in CM. Four sampling sites along Canal La Malaria were analyzed for total metal content and toxic metal fractions were determined using a sequential extraction procedure in the soils of urban aquatic sediments to assess both mobile and potentially mobile toxic metals in Canal La Malaria. Elevated Hg, As, Cd, Cr, and Pb contents were found in sediments (0.421, 9.66, 5.90, 191, and 108 mg/kg (ppm), respectively. A follow up sequential extraction scheme (Tessier 1976) was performed for the three highest concentrations of Cd, Cr, and Pb. Research activities integrate a photogrammetric analysis of historical and topographic maps, high-resolution satellite images. Besides filling fundamental gaps concerning trace metals in a coastal urbanized tropical wetland, results are expected to serve as an early warning of threats to ecosystem resilience.