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The Ogallala aquifer, underlying eight states from South Dakota to Texas, is practically non-recharging south of Nebraska, and groundwater withdrawals for irrigation have lowered the aquifer in western Kansas. Subsequent well-yield declines encourage deficit irrigation, greater reliance on precipitation, and producing profitable drought-tolerant crops like upland cotton (Gossypium hirsutum (L.)). Our objective was to evaluate deficit irrigated cotton growth, yield, and water productivity (CWP) in northwest, west-central, and southwest Kansas in relation to El Niño southern oscillation (ENSO) phase effects on precipitation and growing season cumulative thermal energy (CGDD). Using the GOSSYM crop growth simulator with actual 1961–2000 location weather records partitioned by the ENSO phase, we modeled crop growth, yield, and evapotranspiration (ET) for irrigation capacities of 2.5, 3.75, and 5.0 mmd−1 and periods of 4, 6, and 8 weeks. Regardless of location, the ENSO phase did not influence CGDD, but precipitation and lint yield decreased significantly in southwest Kansas during La Niña compared with the Neutral and El Niño phases. Simulated lint yields, ET, CWP, and leaf area index (LAI) increased with increasing irrigation capacity despite application duration. Southwestern Kansas producers may use ENSO phase information with deficit irrigation to reduce groundwater withdrawals while preserving desirable cotton yields.