Tropical mountainous rivers transport a disproportionate amount of sediment to the global ocean. While these systems also deliver sediment-related pollutants (i.e., metals) to the coast, the potential accumulation of metal contaminants within these systems has been largely unexplored. This study analyzed the trace metal concentrations of fine riverbed sediment (< 0.63 µm) collected from Rio Loco, Rio Yauco and Rio Guamaní in Puerto Rico. A total of 17 samples were collected in June 2019 (~ 21 months following Hurricane Maria) from these watersheds. Metal concentrations (Al, Ba, Cd, Cu, Cr, Fe, Mn, Ni, Sb, Sn, U and Zn) were quantified with acid digestion and inductively coupled plasma mass spectrometry. Strong positive correlations were found between Cd, Pb, Sb and Sn (r avg > 0.60, p < 0.05) as well as between Ba, Cr and Ni (r avg > 0.81, p < 0.05). A comparison of land cover with metal concentrations revealed positive statistical relationships between Cu, Sb, Sn and Zn with developed land and Cr, Ni and U with agricultural land. Between 7 and 50% of the samples exhibited enrichment factor values indicative of moderate to significant levels of contamination (EF > 2) for each metal. Additionally, several metal concentrations exceeded the consensus-based threshold effect and probable effect values. Altogether, these data confirm that metals do accumulate in tropical mountainous watersheds and can be found at concentrations that impact freshwater ecosystems. These elevated metal concentrations coupled with periodic flushing events, regularly supported by hurricanes, suggest a threat to nearshore ecosystems such as coral reefs.