Using multiple sampling techniques we documented the nightly occurrence of benthic macroinvertebrates in the water column, and quantified the intensity of their emergence from and re-settlement back to the benthos, along the seagrass–coral reef interface at two widely separated locations in the Florida Keys National Marine Sanctuary (FLKNMS). Plankton collections consistently documented dramatic increases in benthic invertebrate abundance in the water column after sunset. Subsequent collections using emergence traps showed that the density of benthic invertebrates, emerging from the seagrass habitats was great (often >1000individuals/m2). Settlement traps further revealed that emigrant invertebrates were dispersed by currents and did not necessarily resettle in the same intensity back to the emergence site. Our results show that the nocturnal emergence of benthic invertebrates is widespread and persistent temporally. As a result, we hypothesize that the diurnal emergence of these organisms probably reduces the intensity of food web interactions between benthic organisms and demersal reef fishes that enter nearby seagrass habitats to feed at night. These results further illustrate a need to conduct more studies after sunset in order to develop a better understanding what role diurnal shifts in predator and prey occupancy patterns play in determining the intensity of the transfer of energy and nutrients across adjacent trophic levels in marine food webs.