Marine bivalves are important ecosystem constituents and frequently support valuable fisheries. In many nearshore areas, human disturbance—including declining habitat and water quality—can affect the distribution and abundance of bivalve populations, and complicate ecosystem and fishery management assessments. Infaunal bivalves, in particular, are frequently cryptic and difficult to detect; thus, assessing potential impacts on their populations requires suitable, scalable methods for estimating abundance and distribution. In this study, population size of a common benthic bivalve (the geoduck Panopea generosa) is estimated with a Bayesian habitat-based model fit to scuba and tethered camera data in Hood Canal, a fjord basin in Washington state. Densities declined more than two orders of magnitude along a north—south gradient, concomitant with patterns of deepwater dissolved oxygen, and intensity and duration of seasonal hypoxia. Across the basin, geoducks were most abundant in loose, unconsolidated, sand substrate. The current study demonstrates the utility of using scuba, tethered video, and habitat models to estimate the abundance and distribution of a large infaunal bivalve at a regional (385-km²) scale.