Genetic diversity in East African highland bananas (EAHB, Musa spp.) is very limited and relies on frequent somatic and/ or epigenetic mutations and continuous farmer selections. Considering the market demand and the drought-sensitive nature of EAHBs, it is crucial to improve the resilience of these endemic banana varieties to future environmental conditions through breeding. This study aimed to determine the impact of meiotic recombinations on the variability of water usage, growth and transpiration responses of 16 EAHB progenies to declining soil water content (SWC) in relation to the environment. By monitoring plant transpiration at different time resolutions, we were able to model the water usage in relation to SWC, vapour pressure deficit and light and to determine the genotype-specific transpiration behaviour. Significant differences were observed in water usage, growth vigour and leaf damage. We detected genotype-specific SWC and VPD thresholds at which drought avoidance mechanisms were initiated. Reduced growth vigour and concurring lower leaf area during drought do not necessarily lead to drought tolerance. We deliver a proof of principle that drought tolerance improvement in EAHB populations is possible and the ‘ acuminata’ genome can contribute to “drought tolerance”. The suitability of a given drought tolerant genotype will depend on the prevailing drought scenarios.