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In order to understand how the available water stored prior to planting (ASWp) affects cotton yield and the relative physiological parameters, we designed two ASWp levels in columns, well-watered (P-90) and no watering (P-0), combined with different water management scenarios during the cotton-growing period, 70% of field capacity (FC) during the third leaf to boll opening stage (I-70) and changed the third leaf to flowering stage in 55% of FC and 80% of FC thereafter (I55-80). P-90 enhanced root length density (RLD), surface area density (RSD), and root activity, which in turn increased the efficiency of ASWp usage. A significantly higher leaf water potential, net photosynthesis rate, above-ground dry matter (DM), and yield were found in P-90 than in P-0. Under well-watered conditions, I55-80 had a higher RLD in the 40-120cm layer compared with I-70. However, root mass density (RMD) and DM in I55-80 were significantly decreased that led to marked decreases in yield and, to a lesser extent, in water productivity (WP). Under no watering conditions, yield and WP were significantly increased in I-70 relative to I55-80. It showed that sufficient water in deeper soil layers and a sustained 65-75% of FC could be an appropriate drip irrigation mode for the local cotton field. Copyright (c) 2013 John Wiley & Sons, Ltd.