The greater Everglades ecosystem in South Florida, USA, has been subject to eutrophication by anthropogenic phosphorus (P) inputs from canals draining the surrounding agricultural landscapes. In these naturally karstic, oligotrophic wetlands, diatoms are particularly important components of mat-forming calcareous periphyton assemblages and exhibit predictable responses to environmental variation, making them good indicators of P enrichment. While numerous experimental and long-term studies have established protective P criterion for Everglades Protection Areas (Everglades), the Big Cypress National Preserve (BICY) has not received similar attention. Restoration will increase water flow to BICY. Establishing P-driven ecological thresholds to protect BICY wetlands from further degradation is critical. Comparing diatom assemblage composition and diatom species total P (TP) optima from the BICY to those in the Everglades will help inform whether P-driven ecological thresholds and assessment criteria developed for the Everglades are potentially applicable in the BICY. Here, we present efforts to harmonize diatom taxonomic datasets from the BICY with three published studies from the Everglades1,2,3 and a subset of data collected as part of the Comprehensive Everglades Restoration Plan (U.S. Army Corps of Engineers and the South Florida Water Management District). We discuss strategies used to merge these datasets, including: comparing voucher floras, focusing on core species, and assessing relationships between species traits (e.g., diatom species TP optima). We found positive relationships between BICY and diatom species TP optima from the Everglades studies (R2 = 0.40–0.68; p < 0.01). Although these relationships may be improved with further taxonomic harmonization, inconsistencies between the datasets could be explained by other factors, such as P variability within the datasets and/or underlying variability of species traits within diatom populations. Further research is needed to understand factors that cause diatom species traits to vary over space and time.