Seagrasses often provide important ecosystem functions, including providing nursery habitats for economically important fishes. Halophila ovalis is the most abundant seagrass in the Swan-Canning Estuary, Western Australia, where macroalgal blooms, particularly Chaetomorpha linum, can result in seagrass loss. In this study, fish were sampled using a seine net in H. ovalis meadows, floating C. linum and bare sand, as well as floating detached vegetation, to compare their habitat value for fish communities in the estuarine system. Differences in fish communities across habitats were often dependent on location in the system. Generally, vegetated habitats had different fish communities to each other and to bare sand. During the day, H. ovalis generally had higher abundance and species richness than bare sand, whilst bare sand contained more fish and species than C. linum. At night, bare sand had higher abundance and species richness than H. ovalis. Floating detached vegetation had higher abundance and species richness than bare sand. This suggests that these vegetated habitats play a role for fish in the system, but the findings are not consistent across locations, which may relate to extreme rainfall immediately preceding the study period or other environmental factors.