To identify traits that can be used for genetic improvement of drought tolerance of cassava, panels of diverse lines were subjected to water deficit in field and controlled-environment conditions. Under stress, leaf retention was poorly correlated with storage root weight (SRW), as many genotypes shed lower leaves while maintaining a small set of leaves near the shoot apex. Also, leaf chlorophyll greenness readings were similar in both control and water stressed plants when measured on upper canopy leaves, which permitted many genotypes to maintain canopy-scale photosynthetic capacity during water deficit. Relationships between traits associated with water use [canopy temperature, soil water depletion, and abscisic acid (ABA)] indicated that phenotyping for these traits needs to be carefully timed. Leaf sugar contents were correlated with chlorophyll, but were not consistently correlated with yield. In general, genotypes accumulated substantial starch reserves in stems; among genotypes this was correlated with SRW. This suggests that genotypes with more stem starch are better able to sustain activities during prolonged stress and recover upon rewatering. SRW was negatively correlated with aboveground biomass, an indicator of canopy photosynthesis, and fibrous root weight, whereas it was positively correlated with partitioning index for early-stage storage-root growth (PI). Heritability and variation among genotypes were sufficiently high to predict that response to selection would be successful for several traits, including canopy temperature, ABA, and PI. We conclude that PI at an early stage of stress is a valuable trait for phenotyping cassava drought tolerance.