Low water availability is one of the principal stressors for terrestrial invertebrates in the polar regions, determining the survival of individuals, the success of species and the composition of communities. The Arctic and Antarctic dipterans Heleomyza borealis and Eretmoptera murphyi spend the majority of their biennial life cycles as larvae, and so are exposed to the full range of environmental conditions, including low water availability, over the annual cycle. In the current study, the desiccation resistance and desiccation tolerance of larvae were investigated, as well as their capacity for cross-tolerance to temperature stress. Larvae of H. borealis showed high levels of desiccation resistance, only losing 6.9% of their body water after 12 days at 98.2% relative humidity (RH). In contrast, larvae of E. murphyi lost 46.7% of their body water after 12 days at the same RH. Survival of E. murphyi larvae remained high in spite of this loss (>80% survival). Following exposure to 98.2% RH, larvae of E. murphyi showed enhanced survival at −18°C for 2 h. The supercooling point of larvae of both species was also lowered following prior treatment at 98.2% RH. Cross-tolerance to high temperatures (37 or 38.5°C) was not noted following desiccation in E. murphyi, and survival even fell at 37°C following a 12-day pre-treatment. The current study demonstrates two different strategies of responding to low water availability in the polar regions and indicates the potential for cross-tolerance, a capacity which is likely to be beneficial in the ever-changing polar climate.