The composition and distribution of diatom algae inhabiting estuaries and coasts of the subtropical Americas is poorly documented, especially relative to the central role diatoms play in coastal food webs and to their potential utility as sentinels of environmental change in these threatened ecosystems. Here we document the distribution of diatoms among the diverse habitat types and long environmental gradients represented by the shallow topographic relief of the South Florida, U.S.A. coastline. A total of 592 species were encountered from 38 freshwater, mangrove and estuary locations during two seasonal collections, with highest diversity occurring at sites of high salinity and low water column organic carbon concentration (WTOC). Freshwater, mangrove and estuary assemblages were compositionally distinct but seasonal differences were only detected in mangrove and estuary sites where solute concentration differ greatly between wet and dry seasons. Epiphytic, planktonic and sediment assemblages were compositionally similar, implying a high degree of mixing along the shallow, tidal and storm-prone coast. The relationship between diatom taxa and salinity, water total phosphorus (WTP), total nitrogen (WTN) and WTOC concentrations was determined and incorporated into weighted averaging partial least squares regression models. Salinity was the most influential variable, resulting in a highly predictive model (r2 = 0.97) that can be used to infer changes in coastal freshwater delivery or sea-level rise in South Florida and compositionally similar environments. Models predicting WTN, WTP and WTOC were also strong (r2 = 0.75, 0.75, 0.79, respectively), suggesting that diatoms provide reliable independent inferences of changes in solute delivery to the coastal ecosystem.