A mussel's shell records its history of growth. We investigated variability in the size and shape of mussel shells of Mytilus californianus Conrad (1837) to test the hypothesis that the mussel shell provides information on the contemporary condition of the mussel. Two factors were associated with shape: an epithelial discoloration and the Sr/Ca in the shell nacre. Sr/Ca data distinguished the mussel populations as did a discriminate analysis that included the trace metal ratios; Sr/Ca, Mg/Ca, Mn/Ca, Ag/Ca, Cd/Ca, Ba/Ca, and Pb/Ca. Size varied independently of shape and was not associated with the two factors. However, a null model that describes the morphological variability in height and width suggests that mussel size also plays a central role in partitioning phenotypic variability. These analyses of contemporary factors coupled with analyses of morphological variability holds promise for addressing the functional roles of mussel height and width and what proportion of phenotypic variability can be attributed to environmental factors.