Caridean shrimp are a prominent element of seagrass faunal communities and play an important role in the energy transfer between trophic levels. They are a food source for other organisms and play an integral role in the ecosystem by feeding on algae and assisting with the breakdown of organic matter. Carideans are also fundamental to the marine fishery industry in that they are a food source for potentially valuable juvenile commercial fish. Ectoparasitic isopods (Cymothoida: Bopyridae) that infest caridean shrimps decrease the energy level of the shrimp, resulting in slower reaction time, greater predation rate, slower growth rate, and/or reduced egg production. However, in South Florida, little is known about the distributions and effects of parasitism among caridean shrimp in seagrass habitats. This research investigates the relationship of caridean shrimps and ectoparasitic isopods throughout several marine and brackish basins of coastal South Florida ranging from Lostmans River on the lower southwest mangrove coast through Florida Bay and Biscayne Bay. Samples were collected at the end of the wet season in 2010 and the dry season in 2011 using a 1-m2 throw-trap. Relations among isopods, carideans and environment were determined based on a series of biotic (host preference and availability) and abiotic (salinity, temperature, turbidity, water depth) factors. Bopyrid isopods were most abundant in Manatee Bay and Barnes Sound adjacent to the C-111 canal located in southern Biscayne Bay region and predominantly associated with Hippolyte spp. Logistical regression revealed that the likelihood of parasite presence is associated with higher temperatures, lower salinity, increasing depth, less seagrass coverage and greater macroalgae coverage. The results suggest that increased stressors in an environment, such as anthropogenic runoff, may also negatively impact host resistance to parasitism.