Hurricane Irma made landfall in Cudjoe Key, Florida at 13:00 UTC on the 10th of September 2017 at Category 4 intensity. In the years prior to the hurricane, we had been studying the sponge and mesograzer populations in the shallow flats to the south of the Mote Marine Laboratory’s Elizabeth Moore International Center for Coral Reef Research & Restoration, which is approximately 5 km from Irma’s landfall. These data allowed us the opportunity to compare pre- and post-hurricane features of sponge and mesograzer populations in this habitat. We conducted preliminary surveys in the flats 3 months after the hurricane, which revealed significant damage to the largest individuals of the vase-shaped sponge Ircinia campana. We followed the recovery of this sponge for the next two years, and examined hurricane-induced shifts in population structure. In addition to work with this sponge, we examined the responses of mesograzer populations to the hurricane the year after the hurricane. Several of the mesograzers that we examined showed significant shifts in body size. We discuss these patterns in the context of ecosystem resiliency in the face of major disturbances. We consider our findings in the context of the sponge loop hypothesis, which states that biodiversity in tropical habitats is supported by the detritus-producing capabilities of sponges. Our work highlights short-term and potential long-term impacts of hurricanes on these important tropical marine habitats.