Habitat use during early life history plays an important role in the ecology of smallmouth bass Micropterus dolomieu in north temperate lakes. The highest levels of mortality occur during the first year of life, and the habitat selected probably affects mortality. We used resource selection functions and abundance data from two northern Wisconsin lakes to determine the habitats that influence the survival of smallmouth bass. Coarse substrates were consistently important to both nesting locations and young-of-year smallmouth bass. Young smallmouth bass used woody structure after swimming from their nests but disassociated themselves from habitats with more complex woody structure by August. Nonwoody cobble areas offer protection for young-of-year smallmouth bass without attracting predators, as woody habitats do. The decline in the abundance of young-of-year smallmouth bass was best fit to an exponential decay function in woody habitats, but in rock habitats it was linear. Habitat selection by young-of-year smallmouth bass shifts over time, and the shift is linked to predation risk: woody habitats initially offer them an advantage with respect to spawning but eventually provide their predators greater opportunities for ambush. This shift underscores the importance of having a diversity of littoral habitats. This study provides the first quantifiable analyses describing the habitat features selected by young-of-year smallmouth bass and links these descriptions to population dynamics.