This study assesses the ecological factors associated with microfilariae prevalence in wild populations of endangered flightless cormorants (Phalacrocorax harrisi) and Galápagos penguins (Spheniscus mendiculus). Prevalence values were tested for correlation with a large number of environmental variables, as modeled from weather station data and measured by satellite-borne sensors. Predictions were made based on the expected effects of climatic and landscape variables on sustained populations of arthropod vectors required for transmission of microfilariae. In general, findings were consistent with predictions in both cormorants and penguins; prevalence correlated positively with temperature, precipitation, and vegetation density, and negatively with measures of environmental variability. Resulting correlates were used to derive predictive distributions of prevalence values in cormorants throughout the archipelago. Evidence is presented implicating the mosquito Aedes taeniorhynchus as a likely vector. Knowledge of environmental variables that predict risk of disease transmission by arthropod vectors may be useful in control measures should novel pathogens be introduced to the ecosystem.