The ability of ecosystems to regulate water quality and flood events has been linked to health outcomes, including mosquito-borne illnesses. In the San Juan Bay Estuary watershed of Puerto Rico, habitat alterations and land-use development have disrupted watershed hydrology, exacerbating wastewater discharges and subjecting some neighborhoods to frequent flooding events. In 2016, the mosquito-borne illness Zika became a new cause for concern. We hypothesized that nutrient-enriched flood water could provide pulses of supplemental nutrients to local mosquito populations. We conducted a field study in six neighborhoods adjacent to the estuary to assess whether environmental variability of nutrient inputs could be linked to breeding habitat containers, Aedes aegypti larvae and adults, and the acquisition of Zika virus by adult mosquitoes. The most frequently flooded neighborhood had consistently higher levels of nitrogen in estuary water, leaf detritus, containers, and adult mosquitoes compared to other neighborhoods. Adult body nitrogen was significantly related to both nitrogen content of containers and leaf detritus from the local trapping area. Disseminated Zika concentration in adult Ae. aegypti tended to decrease as body carbon and nitrogen increased. Our study provides preliminary evidence that environmental variability in nutrient inputs can influence viral acquisition by mosquito vectors. This suggests that management actions to reduce flooding and improve water quality should go hand-in-hand with more traditional vector control methods, such as aerial spraying, to help control spread of vector-borne diseases.