Urbanization adjacent to rivers has increased in recent years and is considered a source of environmental contamination. The resulting increase in number of urban rivers in highly populated areas, such as the Caribbean island of Puerto Rico, has led to the appearance of synthetic as well as naturally occurring chemicals not previously observed nor regularly monitored in freshwater habitats. Some of these chemicals, such as heavy metals and plasticizers, have been shown to affect endocrine, respiratory, and nervous system function in animals and humans, even at relatively low concentrations. The purpose of this study was to measure concentrations of such emergent contaminants on rivers of urbanized areas on the northeast of Puerto Rico, as one element in the assessment of the impact of urbanism on water quality in these communities. To accomplish this, we used Inductively Coupled Plasma and Gas Chromatography Mass Spectrometry to measure amounts of heavy metals and phthalates, respectively, in superficial water of three rivers of Puerto Rico: Mameyes (non-urban), Río Piedras (urban river without a dam), and La Plata (urban river with a dam). The urban rivers had significantly higher concentrations of heavy metals arsenic, barium, cadmium, manganese, and antimony, when compared with the reference non-urban river. Manganese was the only metal found in concentrations higher than limits established by the EPA for drinking water. Of eight phthalates amenable to measurement with the chosen protocol and instrumentation, only dibutyl phthalate was detected, only in the La Plata river, and at concentrations ranging from 3 to 8 parts-per-billion. These findings suggest that urbanism close to rivers of Puerto Rico is likely having an impact on water quality and thus further study to identify the potential sources, as well as the inclusion of these emergent contaminants on the list of chemicals regularly monitored by government agencies is justified.