The factors determining the spatial and temporal distribution of West Nile virus (family Flaviviridae, genus Flavivirus, WNV) activity are not well understood. Here, we explore the effects of hydrological and meteorological conditions on WNV infection among Culex genus mosquitoes collected during 2001–2009 in Suffolk County, Long Island, NY. We show that WNV infection rates in assayed pools of Culex mosquitoes are associated in both space and time with hydrological and meteorological variability. Specifically, wet winter, warm and wet spring conditions, and dry summer conditions are associated with the increased local prevalence of WNV among Culex mosquitoes during summer and fall. These findings indicate that within Suffolk County, and for a given year, areas at risk for heightened WNV activity may be identified in advance by using hydrology model estimates of land surface wetness and observed meteorological conditions.