Background Few studies have evaluated the effect of drought on the morpho-physiological characteristics of African C4 grasses. We investigated how drought affects leaf gas exchange characteristics, biomass partitioning, and water use efficiencies of Enteropogon macrostachyus and Cenchrus ciliaris. Methods The grasses were grown in a controlled environment under optimum conditions, that is, 70% of the maximum water-holding capacity (WHC) for the first 40 days. Thereafter, half of the columns were maintained under optimum or drought conditions (30% of maximum WHC) for another 20 days. Results Under optimum conditions, C. ciliaris showed a significantly higher photosynthetic rate, stomatal conductance, and transpiration rate than E. macrostachyus. Drought decreased the photosynthetic rate, stomatal conductance and transpiration rate only in C. ciliaris. The net photosynthetic rate, stomatal conductance, and leaf transpiration of E. macrostachyus did not differ significantly under optimum and drought conditions. E. macrostachyus showed an increase in its water use efficiencies under drought to a greater extent than C. ciliaris. Conclusions Our results demonstrate that C. ciliaris is more sensitive to drought than E. macrostachyus. The decrease in the intercellular CO2 concentration and the increase in stomatal limitation with drought in C. ciliaris and E. macrostachyus suggest that stomatal limitation plays the dominant role in photosynthesis of the studied African C4 grasses