Inputs of detritus have been shown to be strong drivers of container mosquito production and life history traits, including for species that are of medical importance. During 2016, Zika infection swelled throughout the Caribbean and South and Central America, a disease vectored principally by container Aedes. We investigated how inputs of nutrients (carbon, nitrogen) affected Aedes aegypti in San Juan, Puerto Rico in the summer of 2016 during an outbreak of Zika. The San Juan Bay estuary receives inputs of human-associated nutrients that enter neighborhoods during periodic flooding events. We sampled mosquito containers in neighborhoods along the estuary, representing a gradient of nutrients, to determine if they are entering larval containers, and may affect mosquito larvae and subsequently adults. We also determined if differences in nutrients across neighborhoods could explain abundance of mosquitoes and the prevalence of Zika within adult female mosquitoes. We found a relationship between container nutrients and larval body nitrogen and carbon. Furthermore, we found a relationship between estuary nutrients and the abundance and carbon:nitrogen of adults. However, nutrients in containers were not reflective of those from the surrounding estuary, possibly reflecting variability in flood waters, detrital inputs, and container evaporation. For Zika, we tested 110 Aedes aegypti, of which 44 were positive. We found strong relationships between adult body nitrogen and Zika titer, with adults having higher nitrogen content generally having lower titers. Thus, there appears to be a role for nutrients in the production of Aedes aegypti and Zika in Puerto Rico.