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This study aims to analyze agricultural productivity growth by taking into account water endowment in agriculture in sub-Saharan Africa. The true-random Stochastic Production Frontier (SPF) method is used to estimate the agricultural production function incorporating “water endowment” as an input, and to derive the total factor productivity for a sample of nineteen countries over the period 1991–2014. The results of the SPF model show that the coefficients of the classic production factors and water endowment have a positive and significant effect on agricultural output growth after correcting any potential endogeneity bias issues. The average growth rate of total factor productivity (TFP) with “water endowment” is estimated at 0.045 percent per year over the whole period, far lower than the classic TFP estimated at around 1 percent on average per annum. From 1991 to 2001, this rate is negative, estimated at −0.44 percent. It is 0.36 percent over the period 2002–2012. The greater improvement in the last decade is believed to be due to the significant adoption of good agricultural practices thanks to technological advances which have resulted in water savings (i.e., from −0.08 percent to −0.05 percent on average per year). Hence, greater emphasis needs to be placed on water-saving practices essential for efficient water use in agriculture.JEL Codes: O13, Q1, Q3.