In Portovelo in southern Ecuador, 87 gold processing centers along the Puyango-Tumbes River produce an estimated 6 tonnes of gold per annum using a combination of mercury amalgamation and/or cyanidation and processing poly-metallic ores. We analysed total Hg, Hg isotopes, total arsenic, cadmium, copper, lead and zinc in water and sediment along the Puyango in 2012-2014. The highest total mercury (THg) concentrations in sediments were found within a 40 km stretch downriver from the processing plants, with levels varying between 0.78-30.8 mg kg-1 during the dry season and 1.80-70.7 mg kg-1 during the wet season, with most concentrations above the CCME (Canadian Council of Ministers of the Environment) Probable Effect Level (PEL) of 0.5 mg kg-1. Data from mercury isotopic analyses support the conclusion that mercury use during gold processing in Portovelo is the source of Hg pollution found downstream in the Tumbes Delta in Peru, 160 km away. The majority of the water and sediment samples collected from the Puyango-Tumbes River had elevated concentrations of, arsenic, cadmium, copper, lead and zinc exceeding the CCME thresholds for the Protection of Aquatic Life. At monitoring points immediately below the processing plants, total dissolved concentrations of these metals exceeded the thresholds by 156-3567 times in surface waters and by 19-740 times in sediment. The results illustrate a significant transboundary pollution problem involving Hg and other toxic metals, amplified by the fact that the Puyango-Tumbes River is the only available water source in the semi-arid region of northern Peru.