In total, 93,532 female mosquitoes (Diptera: Culicidae) were captured in traps placed in subterranean (catch basin), ground (≈ 1.5 m above ground), and canopy (≈7.0 m above ground) habitats in Stamford and Stratford, CT, during 2003–2005. Culex pipiens L. was the most abundant (64.8%) of the 31 species identified. Significantly greater numbers of Cx. pipiens were captured in canopy-placed mosquito magnet experimental traps, and significantly greater numbers were collected in catch basin-placed (Centers for Disease Control) CDC traps than in CDC traps placed elsewhere. Culex restuans Theobald was captured in significantly greater numbers in traps placed in catch basins. Aedes vexans (Meigen), Aedes cinereus Meigen, and Aedes cantator (Coquillett) were significantly more abundant in ground traps. In total, 429 isolations of West Nile virus (WNV) were made from seven species of mosquitoes from late June through the end of October during 2003 through 2005. Three hundred ninety-eight (92.8%) isolates were from Cx. pipiens. Others were from Cx. restuans (n = 16), Culex salinarius Coquillett (n = 5), Ae. vexans (n = 4), Ae. cantator (n = 3), Aedes triseriatus (Say) (n = 2), and Ae. cinereus (n = 1). Multiple isolates from Cx. pipiens were made each week, primarily during the later part of July through the end of September. Weekly minimum infection rates (MIRs) were lower in 2004 (highest weekly MIR = 7.1) when no human cases were reported in Connecticut in comparison with 2003 and 2005 (highest weekly MIR = 83.9) when human cases were documented. Frequencies of infected pools were significantly higher in Cx. pipiens captured in traps in the canopy and significantly higher in catch basin placed traps than in traps at ground level. The physiological age structure of Cx. pipiens captured in the canopy was significantly different from that of Cx. pipiens collected in catch basins. Invariably, Cx. pipiens captured in the canopy were nulliparous or parous with ovaries in Christophers’ stage 2, whereas 58.7% of the females captured in catch basins possessed ovaries filled with mature oocytes in Christophers’ stage 5. Our results suggest that females in the canopy are seeking hosts, and after digestion of the bloodmeal and development of mature oocytes, they descend to catch basins for shelter and deposition of eggs. WNV was isolated from three, one, and two pools of male Cx. pipiens captured in catch basin-, ground-, and canopy-placed traps, respectively, and from six nulliparous Cx. pipiens females collected in the canopy. Weekly MIR ranged from 1.2 to 31.1 per 1,000 male specimens. These data show that mosquitoes become infected by means other than by blood feeding, possibly by transovarial transmission. The placement of traps in tree canopies and in catch basins can be used to augment current practices of placement of traps near the ground for surveillance of mosquitoes infected with WNV and for studies of the ecology of WNV.