Ecological gradients are one of the main reasons for changes in biodiversity. However, whether what is known to be true for plants and animals also applies to protists in the same way is largely unknown. Along an alpine elevation gradient, including 29 freshwater lakes, we investigated ecological drivers of protistan diversity and community structure, as well as the explanatory value of the species-area relationship for protistan diversity using a deep-sequencing approach. We found that species richness does not decrease with elevation, nor is elevation a major factor explaining the observed shifts in community composition. The observed protistan communities differ depending on many factors, with pH and nutrient concentrations being most important. Considering distinct subgroups, Chrysophyceae accurately reflect the pattern of the overall protistan community. Within the investigated elevation gradient, species richness was correlated with the area of individual lakes irrespective of their elevation. However, we found no support for decreasing species richness with elevation, as known for plants and animals.