Diporeia spp. were a key component of the Great Lakes benthos, converting the pelagic algal rain to secondary production, which is critical for Great Lakes fishes. However, Diporeia declines since the 1980s have been rapid and widespread. While there are temporal relationships between Diporeia declines and spread of zebra and quagga mussels, establishing a mechanistic link has been difficult. Diporeia declines may result from competition for food resources with dreissenid mussels; however, conflicting evidence suggests food limitation may not be the direct link. To test food limitation, we analyzed gut contents of Diporeia collected between the 1980s and 2009 from two deep (>100 m) and one nearshore station (~50 m depth) in southern Lake Michigan. We further analyzed sediment cores from the same stations to resolve relationships among food resources, Diporeia diet, and diet selectivity during pre- and post-dreissenid invasion. In spring, pre-dreissenid Diporeia fed selectively and exclusively on large (Stephanodiscus) and filamentous centric diatoms (Aulacoseira). Diporeia diets showed significant shifts during the 2000s to greater proportions of small centric and araphid diatoms, coincident with Diporeia declines and offshore expansion of quagga mussels. Sediment cores recorded declines in Aulacoseira and large Stephanodiscus from 1960 to 2009 and increases in small centrics after dreissenid introduction. Accounting for high selectivity in springtime Diporeia diets, community changes in sediment records are consistent with changes observed in Diporeia diets and suggest Diporeia declines have been exacerbated by a shift from more nutritious and highly preferred diatom species to less nutritious and negatively selected species.