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Nearshore benthic habitats of Biscayne Bay fit the prediction of communities at risk due to their location adjacent to a large metropolitan center (Miami) and being influenced by changes in hydrology through the activities of the Comprehensive Everglades Restoration Plan (CERP). We examine whether the proposed programmatic expansion of mesohaline salinities through the introduction of additional fresh water would result in: (1) increases in seagrass cover; (2) expansion in the distribution and cover of Halodule; and (3) a reduction in the dominance of Thalassia, as hypothesized by CERP. Seagrasses were present at 98 % of sites where they covered 23 % of the bottom. Salinity was the only physical variable with a significant relationship to the occurrence of all SAV taxa. Occurrence of Thalassia, Halimeda, and Penicillus increased significantly with increasing salinity, but Halodule, Syringodium, Laurencia, Udotea, Batophora, Caulerpa, and Acetabularia showed a significant negative relationship with salinity. Mesohaline habitats had higher cover of seagrass and Halodule, and reduced dominance by Thalassia. Thus, we expect increases in the extent of mesohaline habitats to achieve the established CERP goals. We also examined the nutrient content of seagrass blades to evaluate whether: (1) nutrient availability is higher in areas close to canal discharges; and (2) tissue nutrient levels are related to seagrass abundance. The low abundance of Thalassia along the shoreline is not only due to its exclusion from low-salinity environments but also by higher nutrient availability that favors Halodule. Percent N and P, and N:P ratios in seagrass tissue suggest that Biscayne Bay receives high N inputs and is P-limited. Thus, increased P availability may facilitate an expansion of Halodule. The data presented suggest that increased mesohaline salinities will increase seagrass abundance and support co-dominance by Halodule and Thalassia as hypothesized, but raise concerns that current high N availability and increases in P may prompt a shift away from seagrass-dominated to algal-dominated communities under scenarios of enhanced fresh water inputs.