In small and spatially isolated forest fragments, increased homozygosity may directly affect individual tree fitness, through the expression of deleterious alleles that influence morphological and physiological traits. Climate change induced drought may exacerbate the detrimental genetic consequences of forest fragmentation because the fitness response to low levels of heterozygosity is generally thought to be more pronounced under environmental stress than under optimal conditions. To test this hypothesis, we performed a greenhouse experiment in which fitness traits of 6-months-old seedlings of Quercus robur, differing in multi-locus heterozygosity (MLH), were recorded during 3 months under both a well-watered and a drought stress treatment (50 seedlings per treatment). Heterozygosity-fitness correlations (HFC) were examined by correlating transpiration parameters and various growth traits of individual trees to their MLH and by studying their response to drought stress. We obtained weak, but significant effects of the MLH ( = 3–11%, p < 0.05) on several fitness traits. High atmospheric stress (e.g. high vapor pressure deficit (VPD) influenced the strength of the HFCs of the transpiration parameters, whereas only a limited effect of the irrigation treatment was observed. Considering ongoing climate change, increased VPD levels in the future may strengthen the negative fitness responses of trees to low MLH.