The objective of this study was to investigate the effect of nitrogen (N) management on soil water recharge, available soil water at sowing (ASWS), soil water depletion, and wheat (Triticum aestivum L.) yield and water use efficiency (WUE) after long-term fertilization. We collected data from 2 experiments in 2 growing seasons. Treatments varied from no fertilization (CK), single N or phosphorus (P), N and P (NP), to NP plus manure (NPM). Comparing to CK and single N or P treatments, NP and NPM reduced rainfall infiltration depth by 20–60 cm, increased water recharge by 16–21 mm, and decreased ASWS by 89–133 mm in 0–300 cm profile. However, crop yield and WUE continuously increased in NP and NPM treatments after 22 years of fertilization. Yield ranged from 3458 to 3782 kg/ha in NP or NPM but was 1246–1531 kg/ha in CK and single N or P. WUE in CK and single N or P treatments was < 6 kg/ha/mm but increased to 12.1 kg/ha/mm in a NP treatment. The NP and NPM fertilization provided benefits for increased yield and WUE but resulted in lower ASWS. Increasing ASWS may be important for sustainable yield after long-term fertilization.