The ability of heterotrophic flagellates to survive and adapt to increasing salinities was investigated in this study. Whole soil samples were subjected to salinities corresponding to marine conditions and clonal cultures were used to perform growth and adaptation experiments at a wide range of different salinities (0–50 ppm). More morphotypes tolerant to elevated NaCl levels were found in road verge soil that was heavily exposed to de-icing salt than in less exposed soils, though there were fewer tolerant than intolerant morphotypes in all soils examined. Heterotrophic flagellates isolated on a freshwater medium from a non-exposed soil were unable to thrive at salinities above 15 ppt, and showed reduced growth rates even at low salt salinities (1–5 ppt). The findings suggest that heterotrophic soil flagellates are less tolerant to NaCl than their aquatic relatives, possibly due to their long evolutionary history in soil, and support the idea that identical morphospecies may differ considerably with respect to physiology