The intertidal cockle, Austrovenus stutchburyi (the little neck clam) occurs throughout New Zealand in sheltered sandflats and estuaries. Over the past 30 years populations have declined and cockle populations in the Canterbury area are exposed to a variety of potential contaminants and stressors. Population structure and cockle density were recorded from 8 intertidal sites between January 2006 through to October 2007. Few cockles reach a marketable size of 30mm shell length, populations are highly variable with irregular recruitment success. Low numbers of small (juvenile) individuals support the observation of populations in decline. Density and mean cockle length did not correlate with sediment-bound trace metal concentration, salinity or silt content but maximum shell length decreased with increasing sediment nitrogen levels. A combination of factors is most likely responsible for determining the population structure. Trace metal tissue concentrations from cockles collected from 4 of these sites were site specific and related to contaminant loads. Accumulated trace metals in tissues did not exceed safety guidelines for human consumption, but bacterial or viral contamination could be an issue.