Restored estuaries in southern California are limited in size and shape by fragmentation from human development, which can in turn restrict habitat use. Thus, it is important to assess how habitat design affects how fish use restored estuaries. Acoustic telemetry tracking from prior studies revealed that Gray Smoothhounds (Mustelus californicus) used primarily the eelgrass ecotone and warm interior waters in Bolsa Chica Full Tidal Basin (BCFTB), a 1.48 km² open-format marine dominated estuary. In this study, M. californicus utilized the Channel in Huntington Beach Wetlands Complex (HBWC), a smaller creek estuary. The Channel had more eelgrass than other available habitats but was also the coolest microhabitat, with temperatures below what M. californicus was found to select in BCFTB. Individuals may behaviorally thermoregulate by moving upstream, away from the HBWC Channel, during periods of incoming, cooler ocean water. Mustelus californicus translocated to different microhabitats within the HBWC selected the Channel habitat after the translocation regardless of where animals were released. Despite the large difference in available subtidal habitat between HBWC and BCFTB, no differences in patch size utilization distributions of M. californicus were observed. While individuals seem to shift between microhabitats based on temperature and eelgrass availability, the area size used by M. californicus appears to be the same within both sites despite the differences in overall size between sites. These results suggest that differences in microhabitat use may influence distribution patterns of M. californicus within each site, and therefore, shark abundance may vary with the restoration design (e.g. basin versus channel) and the size of the estuarine habitat. This information on habitat selection will be critical to planning future restorations on the Southern California coast.