Worldwide, shellfish beds are declining and are threatened by anthropogenic changes. Although the little neck clam Austrovenus stutchburyi supports commercial harvesting, little is known about the population status of this burrowing venerid bivalve in many parts of New Zealand. Populations were sampled seasonally (4 times each year) for 3 y and then during the summer for an additional 4 y within 4 estuarine systems in the Canterbury region of South Island. The aim was to determine population density and class size composition, comparing high-salinity and low-salinity sites with a range of contaminant inputs. The data presented cover pre- and postearthquake events (earthquake sequence commenced on September 4, 2010). Our results show both temporal and spatial variation in population size with irregular recruitment success (0–70 juveniles/m²) across all sites. Density (range, 100–3,500 clams/m²) and mean clam length (range, 17.4–31.6 mm) did not correlate with salinity, sediment trace metal concentration, silt content, nutrient concentration, or anthropogenic land use. A combination of factors and multiple stressors are most likely responsible for determining the population structure and abundance of this species.