Decaying and partially silica-permineralized subfossil plant stems collected from geothermally influenced wetlands of Yellowstone National Park contain evidence of colonization by protists, including heliozoa and chrysophytes. Wetland pools in which the plants and heliozoans occur represent an extreme environment characterized by steady influxes of hot-spring water. Recorded physicochemical conditions in wetland pools reveal relatively high temperatures (often >35 °C), high pH (≤9.1), high conductivity (>3000 µS/cm−1), brackish salinity and elevated concentrations of toxic elements including antimony (Sb), thallium (Tl), mercury (Hg), and arsenic (As). This report contains the first observations of heliozoans and chrysophytes from intercellular sites within decaying plants and adds a previously unreported and extreme environment to their known habitats. Such settings are potential taphonomic windows for preservation of fossil protists.