Stable oxygen (δ18O) isotopic measurements of marine shell carbonate are useful proxies for reconstructing past marine conditions on time scales that are relevant for archaeological interpretations. This includes long-term changes in sea surface temperature (SST) and estimates of the season of harvest of shells, with implications for site seasonality and mobility. As these studies are applied with more frequency, it becomes important to look at relevant details of the ecology of the species that is being tested. We conduct an experimental study on Mytilus californianus (California mussel) shells from a piling on the pier at Bechers Bay on Santa Rosa Island, California to assess the effects of vertical position in the water column on shell length, δ18O, and stable carbon (δ13C) isotopic measurements. Shell length has the most substantial relationship of the three. It increases with depth and therefore time spent submerged, up to a maximum point. This difference can be as much as 45%. δ18O has a statistically significant negative trend with depth, which can result in an offset of 1.8 °C in extreme cases. δ13C does not have a clear pattern with depth. This study indicates that while stable isotopic measurements of California mussel shells can still be used in paleoenvironmental reconstructions, it is necessary to be aware of additional error sources in estimates of annual SST ranges and ideally, interpretations of season of harvest of an individual shell should be made independently from other shells.