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Harmful algal blooms (HABs) are a reoccurring threat to subsistence and recreational shellfish harvest in Southeast Alaska. Recent Tribally led monitoring programs have enhanced understanding of the environmental drivers and toxicokinetics of shellfish toxins in the region; however, there is considerable variability in shellfish toxins in some species, which cannot be easily explained by seasonal bloom dynamics. Persistent concentrations of paralytic shellfish toxins (PSTs) in homogenized butter clam samples (n > 6, Saxidomus gigantea) have been observed in several communities, and relatively large spikes in concentrations are sometimes seen without Alexandrium observations or increased toxin concentrations in other species. In order to investigate potential sources of variability in PST concentrations from this subsistence species, we assessed individual concentrations of PSTs across a size gradient of butter clams during a period of relatively stable PST concentrations. We found that increasing concentrations of PSTs were significantly associated with larger clams using a log-linear model. We then simulated six clams randomly sampled from three size distributions, and we determined large clams had an outsized probability of contributing a significant proportion of the total toxicity in a six-clam homogenized sample. While our results were obtained during a period of low HAB activity and cannot be extrapolated to periods of intoxication or rapid detoxification, they have significant ramifications for both monitoring programs as well as subsistence and recreational harvesters.