This study describes changes in abundance of hyperbenthic zooplankton (including meroplankton) and benthic colonists at the seasonally hypoxic seabed of Saanich Inlet, British Columbia, Canada. We used the Victoria Experimental Network Under the Sea (VENUS) cabled observatory to measure water properties and to sample hyperbenthos with a sediment trap at 97 m from September 2008 to September 2009. Some faunal groups exhibited seasonal reproduction, and abundance peaked during their reproductive periods. These included larvae of the barnacle Balanus crenatus, and the crabs Petrolisthes eriomerus, Oregonia gracilis, and Lophopanopeus bellus bellus. Other groups were most abundant in spring and summer when food and oxygen levels were highest and temperature was lowest. These included cumaceans, the siphonophore Diphyes sp., the bryozoan Triticella pedicellata, and tintinnids. We also collected benthic colonists, predominantly bryozoans and polychaetes, on colonization plates deployed in spring/summer 2008, fall 2008/winter 2009, and spring/summer 2009. The total abundance of colonists and of bryozoans did not vary seasonally or with substrate complexity, whereas polychaetes were more numerous in spring/summer deployments and on a highly complex substrate. Taxon richness of colonists was higher in spring/summer 2008 than in fall 2008/winter 2009, whereas an anoxic episode in spring/summer 2009 reduced richness to similar values with that of fall 2008/winter 2009 levels. Substrate complexity had no effect on richness. Juvenile squat lobsters, digitally imaged in fall 2008/winter 2009, were most numerous when oxygen levels were lowest and potentially excluding larger predators. Our study illustrates how season, food availability, temperature, and oxygen can interact to shape community structure in a seasonally hypoxic habitat.