Salterns consist of a series of interconnected evaporators that form sectors in the salterns. Their operation generates an increasing saline gradient, which influences species diversity. The present study was conducted in three salterns, with the goal of evaluating the diversity partitioning of phytoplankton along the saline gradient. We identified 65 taxa; the species richness was similar among the salterns, with higher values occurring in initial sectors and a downward trend with increasing salinity. In the partitioning analysis, the a diversity contributed 33.8% of the total diversity. The diversity variance showed a strong reduction from the a to ß1 (33.8–6.3%). At higher scales, the highest species richness was found between salt marshes; however, there was lower diversity and a decrease in similarity from the lower to the higher scale. Therefore, we demonstrated that the greater variance in phytoplankton richness was at higher scales.