The endangered June sucker, Chasmistes liorus, is a long-lived, zooplanktivorous sucker endemic to Utah Lake, Utah. Habitat degradation both in the tributaries, where adults spawn, and in the lake has contributed to near complete mortality of larval and juvenile fish within the first few weeks after hatching, leading to a long-term lack of recruitment to the adult population. Recovery of June sucker depends on habitat restoration in the river and the lake that will increase the survival of young fish. Thus, it is important to understand how habitat heterogeneity within the lake will influence the survival and growth of young June suckers. To this end, we compared the survival and growth of juvenile June suckers at 2 spatial scales: (1) large regions across the lake and (2) habitats within regions, namely, open water versus vegetated habitats. We related patterns of survival and growth to food availability (zooplankton density). Growth, but not survival, differed significantly among sites at the landscape scale. Sites with higher zooplankton density had higher mean growth. At the habitat scale, survival was greater in vegetated habitats, whereas growth was higher in the open water. Again, increased growth occurred in the area where zooplankton density was greatest. The density of small zooplankton (e.g., Brachionus rotifers) is a good indicator of habitat suitability for young June suckers at both the regional scale and the habitat scale. Future restoration activities should focus on submersed macrophytes and the spawning tributaries (e.g., Hobble Creek) that transport larval fish into the most productive regions of Utah Lake with the highest zooplankton densities (e.g., Provo Bay).