Stable isotopes recorded in fish eye lenses are an emerging tool to track dietary shifts coincident with use of diverse habitats over the lifetime of individuals. Eye lenses are metabolically inert, sequentially deposited, archival tissues that can open avenues to chronicle contaminant exposures, diet histories, trophic dynamics and migratory histories of individual fishes. In this study, we demonstrated that trophic histories reconstructed using eye lenses can resolve key uncertainties regarding diet and trophic habitat shifts. Clear Lake Hitch Lavinia exilicauda chi, a threatened cyprinid, inhabits a single lake (Clear Lake, Lake County, California) and utilizes tributary streams for reproduction. Bayesian mixing models applied to δ13C and δ15N recorded in eye lenses uncovered ontogenetic diet shifts that corresponded with shifts in occupation of habitats providing spawning (tributary streams), rearing (littoral lake), and growth (pelagic lake) functions. The reconstruction of size-structured trophic and habitat information can provide vital information needed to manage and conserve imperiled species such as the Clear Lake Hitch.