Understanding the dynamics of seasonal epizootics of vector-borne pathogens infecting multiple host species presents several challenges. The transmission potential of competent hosts depends on factors influencing the contact rate between hosts and vectors. Feeding preferences of vectors can determine which host species drive the prevalence of infection throughout the overall population, although that species might be a tiny fraction of the competent population. To explore this, we developed a mathematical model for Eastern equine encephalitis (EEE) virus in bird-feeding mosquitos (Culiseta melanura) and perching birds in freshwater hardwood swamps in the Northeastern U.S. We examined the impact that vector feeding preferences, host community structure, and seasonal changes in host populations have on pathogen transmission. We measured strong feeding preference by Cs. melanura for wood thrush (Hylocichla mustelina) and common grackle (Quiscalus quiscula). We show that these feeding preferences result in increased prevalence of EEE in mosquitos and thus risk of spillover throughout the course of the season.