Sockeye salmonOncorhynchus nerkaspawn in many streams and along lake beaches of the Kvichak River system in Alaska, but fry from the distinct spawning areas reside in a common nursery habitat, Iliamna Lake. In addition, Kvichak River subpopulations have similar dates of adult entry into fresh water, similar migration distances, and similar spawning dates. These similarities in rearing environments and migratory timing enabled us to test the hypothesis that differences in spawning and incubation habitat alone can promote differentiation in traits associated with reproductive success. River-spawning sockeye salmon tended to be larger at age and older than those spawning along island beaches. Females from rivers were more fecund but had smaller eggs than the beach-spawning females. Males from beaches were deeper-bodied and (in one comparison) had relatively longer lower jaws than males from rivers. The tendency of river-spawning females to mature later than beach spawners may be related to a higher marine growth rate and greater increase in fecundity with length. Differences in male morphology may reflect the countervailing pressures of natural and sexual selection. We conclude that these patterns of variation reflect, in part, adaptations to spawning and incubation conditions of the populations.