Background: Effects of abiotic and biotic stresses on plant photosynthetic performance lead to fitness and yield decrease. The maximum quantum efficiency of photosystem II (Fv/Fm) is a parameter of chlorophyll fluorescence (ChlF) classically used to track changes in photosynthetic performance. Despite recent technical and methodological advances in ChlF imaging, the spatio-temporal heterogeneity of Fv/Fm still awaits for standardized and accurate quantification. Results: We developed a method to quantify the dynamics of spatial heterogeneity of photosynthetic efficiency through the distribution-based analysis of Fv/Fm values. The method was applied to Arabidopsis thaliana grown under well-watered and severe water deficit (survival rate of 40%). First, whole-plant Fv/Fm shifted from unimodal to bimodal distributions during plant development despite a constant mean Fv/Fm under well-watered conditions. The establishment of a bimodal distribution of Fv/Fm reflects the occurrence of two types of leaf regions with contrasted photosynthetic efficiency. The distance between the two modes (called S) quantified the whole-plant photosynthetic heterogeneity. The weighted contribution of the most efficient/healthiest leaf regions to whole-plant performance (called Wmax) quantified the spatial efficiency of a photosynthetically heterogeneous plant. Plant survival to water deficit was associated to high S values, as well as with strong and fast recovery of Wmax following soil rewatering. Hence, during stress surviving plants had higher, but more efficient photosynthetic heterogeneity compared to perishing plants. Importantly, S allowed the discrimination between surviving and perishing plants four days earlier than the mean Fv/Fm. A sensitivity analysis from simulated dynamics of Fv/Fm showed that parameters indicative of plant tolerance and/or stress intensity caused identifiable changes in S and Wmax. Finally, an independent comparison of six Arabidopsis accessions grown under well-watered conditions indicated that S and Wmax are related to the genetic variability of growth. Conclusions: The distribution-based analysis of ChlF provides an efficient tool for quantifying photosynthetic heterogeneity and performance. S and Wmax are good indicators to estimate plant survival under water stress. Our results suggest that the dynamics of photosynthetic heterogeneity are key components of plant growth and tolerance to stress.