The effects of climate variability, drain spacing, and growing season operational strategy on annual drain flow and crop yield were studied for a hypothetical drainage water management (DWM) system at Purdue University's Water Quality Field Station using the DRAINMOD model. Drainage water management showed potential for reducing annual average (1915–2006) drain flow from all drain spacings (10–35 m) regardless of the growing season operational strategy, with reductions varying between 52 and 55% for the drain spacings considered. Approximately 81 to 99% of the annual drain flow reduction occurred during the non-growing season, depending on the operational strategy. Fixed DWM operational strategies led to an increase in mean predicted yield for narrower spacings compared with conventional drainage systems. Maximum yield was achieved with no control for drain spacings wider than 20 m in 50% of the years. Overall, the height of control had more influence on relative yield than the date of initiation of control. The greatest positive impacts of DWM on relative yield (1.2%) occurred in cool, dry years, while the greatest average negative impacts (−0.2%) occurred in cool, wet years. On average, with the best-case operation selected for annual weather conditions, DWM increased relative yield by approximately 0.8, 0.4, and 0.2% for the 10-, 20-, and 30-m drain spacing, respectively. Accumulated growing degree days and antecedent precipitation index show promise for identifying appropriate operational strategies for DWM.