Marine protists in the eastern Bering Sea (EBS) are understudied despite being a critical component of the productive subarctic ecosystem. Climate change, and particularly the loss of sea ice, is rapidly altering this ecologically vulnerable and economically important system. In this study, the EBS protist community was characterized across recent years with drastic differences in sea ice extent. In 2019, when the extent of sea ice was anomalously low and retreat occurred early, increased fall water temperatures and surface salinities were observed, and the protist community was dominated by apicomplexan parasites. In contrast, 2017 had more typical winter sea ice conditions and in the fall, water temperatures and surface salinities were lower and protist communities were more diverse, with a larger ratio of primary producer to consumer protists compared to 2019. Surface water temperature was identified as a key predictor of apicomplexan compositional abundance and may be important in the life histories of parasites and their hosts. The interannual variability observed here indicates that the transfer of energy and biomass through the EBS ecosystem can differ drastically across years with differential sea ice influence and highlights the need to monitor protist communities and explore the impacts of protistan parasites.