Fluid inclusion water isotope measurements in speleothems have great potential for paleoclimate studies, as they can be used to provide reconstructions of precipitation dynamics and land temperature. Several previous observations, however, suggest that inclusion waters do not always reflect the isotopic composition of surface precipitation. In such cases, dripwaters are thought to be modified by evaporation in the cave environment that result in more positive d2H and d18O values and shallow d2H/d18O slopes. Although evaporation can occur in cave systems, water can also be lost to evaporation during analysis but before water extraction. Here, we examine the likelihood of this possibility with a stalagmite from Borneo. We demonstrate that many samples loose water, and that water loss is controlled by the type and size of inclusions. With multiple replicate measurements of coeval samples, we calculate an evaporative d2H/d18O slope of 1±0.6 (2SE). This value is consistent with model predictions of evaporative fractionation at high analytical temperature at low humidity. Finally, we provide a robust and physically based correction method. We find that fluid–calcite d18O paleotemperatures calculated with corrected d18O data show excellent agreement with recent microthermometry temperature estimates for Borneo during the last deglaciation, suggesting minimal variations in stalagmite d18O disequilibrium over time. Similarly, corrected fluid inclusion d18O and d2H values follow the expected hydroclimate response of Borneo to periods of reduced Atlantic Ocean meridional overturning circulation. Our results suggest that careful petrographic examination and multiple replicate measurements are necessary for reliable paleoclimate reconstructions with speleothem fluid inclusion water isotopes.