Resource managers use habitat restoration to offset estuarine habitat loss; however, there is limited information about how functionally successful restorations have been, particularly with respect to their use by mobile marine predators. Restoration monitoring efforts typically use point-of-capture metrics to assess fish community recovery and habitat use, but this provides little insight into how fish habitat use changes through time. Using translocation experiments, we integrated the movements of California Halibut Paralichthys californicus, a conservation target species, into a point-of-capture monitoring program in a restored tidal creek estuary. Large halibut (>25 cm) were captured more frequently in the main stream channel, while small ones (<25 cm) were typically caught in the innermost marsh creeks. We actively tracked these fish (n = 20; size range = 26.6–60.5 cm TL) acoustically to identify their preferred habitats and challenged these habitat associations by means of translocations to a different habitats. Large fish tended to have small localized convex hull activity spaces, remaining in areas with high water flow and sandy substratum near eelgrass Zostera marina beds. Individuals that were translocated to marshes returned to the channel and exhibited movements over long distances from their initial locations to their last tracked positions; however, fish that were translocated from marshes to the channel remained in channel habitat and moved smaller distances between their first and last tracked points. Large halibut likely selected the channel because higher water flow would lead to higher concentrations of prey. Small halibut used marshes more frequently, likely because marshes have temperatures thought to maximize growth rates. Our study can serve as a proof of concept that linking point-of-capture and tracking data provides valuable information for habitat restoration, including the fact that California Halibut utilize estuaries in a size-segregated manner based on environmental conditions. This suggests that tidal creek estuaries with a variety of channel types and morphologies—like our study site—are well-suited to support this species.