Although semi-isolated mangrove lagoons are common in the Caribbean, few studies have surveyed organisms of multiple trophic levels and taxa in these lagoons, which are characterized by a lack of adjacent seagrass and coral-reef habitats. In this study, visual surveys, minnow traps and plankton tows, which were deployed at abutting mangrove prop roots and on macro-algal beds 5 and 15 m away from the prop roots, were used to study assemblages of fish and their potential prey in a semi-isolated lagoon located on Utila, Honduras during the dry season. Assemblages of fish and macro-crustacea differed between the three distances from prop roots, while zooplankton abundances were highly variable and did not follow any distinct distribution patterns. Daytime visual surveys found that large lutjanid (snapper) juveniles, tetraodontid (pufferfish), and some species of brachyurans were more abundant near prop roots. Small lutjanid juveniles were also significantly more numerous near prop roots, but their potential prey, copepods, showed no such difference in abundance. However, 24-hour minnow trap catches found that mean fish abundance (although low) did not differ between near-mangrove transects and transects located in algal beds away from prop roots. Whereas it is well known that mangrove–seagrass habitats play a vital role for fish in open systems, low abundances of organisms in algal beds, particularly in the day time, in this study indicate that algal beds may not be as important to fish in a semi-isolated mangrove lagoon.