Terminal or intermittent drought stress is a major production constraint to common bean in the tropics. Development of drought adapted bean varieties is a key strategy to minimize crop failure and improve food security in the face of climate variability and change. Previous research indicated that genetic improvement in drought resistance also improves tolerance to low phosphorus availability in soil and also yield potential under favorable growing conditions. But the physiological basis of this improved genetic adaptation was not defined. Field trials were conducted at CIAT-Palmira, Colombia over three seasons from 2007 to 2009 (June to September) to identify key physiological traits that are associated with improved drought resistance of elite lines from the breeding program. Each trial included 36 genotypes that were planted in a 6 x 6 balanced lattice design with 3 replicates. Two levels of water supply (irrigated and rainfed) were applied. Over the three seasons, 2007 and 2008 resulted in intermittent drought stress while 2009 had terminal drought stress conditions. A number of plant attributes were measured including leaf chlorophyll content (SPAD), canopy temperature depression (CTD), leaf area index, canopy dry weight per area, shoot TNC (total nonstructural carbohydrates) content, pod partitioning index, stem biomass reduction and pod harvest index. We identified six small seeded common bean lines (SEN 56, NCB 226, SER 113, SER 125, NCB 280 and SER 128) that were outstanding in their adaptation to drought stress conditions. The superior performance of these lines under drought stress was associated with higher values of leaf area index, canopy biomass, pod partitioning index, and pod harvest index. Correlation coefficients and principal component analysis indicated the importance of traits such as pod harvest index as a selection method in addition to seed yield for improving genetic adaptation of common bean to drought stress.