Habitat restoration planning and design can be informed by information on spatial patterns in habitat use, which can be obtained from temporally and spatially extensive monitoring efforts. Using records from long-term monitoring in four tidal deltas, we modeled how landscape features (channel types, wetland vegetation types, and a channel network connectivity index) influenced juvenile natural-origin (NOr) and hatchery-origin (HOr) Chinook salmon presence/absence and density when present. Models detected strong effects of landscape characteristics on either presence/absence or density, although the directionality and relative importance of these features differed between NOr and HOr fish. In addition, while interannual differences were stronger for NOr juveniles, the seasonal pattern was much stronger for HOr fish and was in fact the strongest predictor of density. For both types of fish, interactions between landscape features and seasonal pattern existed, indicating that habitat use changed dynamically from the beginning to the end of the rearing period. These findings help provide general principles for prioritizing location and designing habitat restoration projects.