Bean crops can be displaced to marginal areas or face abiotic stresses such as water deficit. Physiological responses allow the identification of tolerant genotypes and lead to more precise breeding strategies. The objective of this research was to evaluate the physiological (leaf gas exchange properties, leaf water content, and leaf thickness) and biochemical [proline and malondialdehyde (MDA)] responses of five common bush bean (Phaseolus vulgaris L.) cultivars (ICA-Cerinza, ICA-Bachue, NUA35, Bianca, and Bacatá) under a water shortage period by irrigation suspension (15 days) at two different phenological stages [vegetative: 40–55 days after seed emergence (DAE) or reproductive: (50–65 DAE)]. A completely randomized block design was carried out with a factorial arrangement (the phenological stage as the main factor and the cultivars as the secondary factor) for a total of 10 treatments with four repetitions per treatment. Leaf photosynthesis (Pn) showed equal photosynthesis values in control plants of all cultivars (≈20 μmol·m−2·s−1). The water deficit period reduced Pn close to 55% (≈12 μmol·m−2·s−1) at both, vegetative, or reproductive stage in all cases. Similar results were also observed on leaf thickness, with a reduction of ≈10% in water-stressed plants at either vegetative or reproductive stage in all evaluated cultivars. A higher MDA and proline production were observed in plants affected by a 15-day water deficit period, mainly at the vegetative stage. The obtained results suggest that the vegetative stage presented a more negative impact on the evaluated physiological variables in most of the cultivars used. Cultivar Bachue showed lower gas exchange properties affectation and higher proline content, which may indicate that this cultivar can be tolerant to water deficit stress conditions. This study allows suggesting that proline and MDA estimation are simple, fast, and low-cost techniques to screen cultivars to obtain more precise breeding selection in common bean. Finally, common bean cultivar selection through the use of biochemical markers can be complemented by the estimation of leaf gas exchange parameters at different phenological stages.