Many ecologically generalized populations are composed of relatively specialized individuals that selectively consume a subset of their populations diet, a phenomenon known as individual specialization. The Niche Variation Hypothesis posits that this individual specialization can arise during ecological release if niche expansion occurs mainly through diet divergence among individuals, leading to greater morphological variation. Most tests of this hypothesis have searched for correlations between niche width and morphological variance, but this approach rests on the untested assumption that within-population morphological diversity is highly correlated with ecological diversity. Here, we test whether intrapopulation diet variation is correlated with intrapopulation morphological variation, across 12 lacustrine populations of three-spine stickleback. First, we use behavioral observations, isotopes, and gut contents to show that, within populations, individuals differ in microhabitat use and diet. Second, we show that some populations exhibit more diet variation than others, as evidenced by differences in both isotopic and gut content variation among individuals. Finally, we confirm that populations with greater dietary variation are more morphologically variable. However, this relationship is only significant when total morphological variance is examined, not for individual morphological traits. This discordance may reflect among-population differences in the relationship between individual morphology and diet. Because morphologydiet relationships can differ among populations, morphological variance may be a poor predictor of actual diet variation when diverse populations are being compared.