We investigated which fish species and environmental variables were associated with the invasive round goby (Neogobius melanostomus) and tubenose goby (Proterorhinus marmoratus) in nearshore Canadian waters of the Huron-Erie corridor of the lower Great Lakes. We measured a suite of environmental variables and used triplicate beach seine samples to collect fishes in summer 2006. Thirty sites were sampled in the day and a subset (n = 14) at night. Of 1,955 individuals caught in daytime samples, round goby (21.0 %), spottail shiner (17.3%) and emerald shiner (14.2%) were most abundant. Of 1,521 individuals collected at night, the most abundant species were round goby (42.3%) and emerald shiner (24.1%). Tubenose gobies represented 1% and 1.7% of all individuals caught in the day and night, respectively. Rarefaction analysis showed that overall species richness was greater in the day than night. Significantly more emerald shiner (P = 0.017), rock bass (P = 0.046) and round goby (P = 0.035) were caught at night than in the day; more logperch were caught in the day than at night (P = 0.042). Round gobies were positively associated with water temperatures up to 24°, but there was no relationship between round goby abundance and warmer temperatures. There were too few tubenose goby captured to determine their statistical association with environmental factors; however, tubenose gobies were found only where round gobies were collected. Round goby and tubenose goby were associated with yellow perch and rock bass. The benthic round goby was the most abundant species, whereas other abundant species were pelagic, schooling fishes that occupied a habitat distinct from round goby.