Continuous or discontinued manure applications to agricultural soils may impact soil organic carbon (SOC) and water balances because of manure carbon inputs and the potential for manure-induced soil hydrophobicity (SH) and soil water repellency (SWR). A laboratory study was conducted using a long-term (44 yr) field experiment on a clay loam soil to determine the effect of application rate of feedlot manure under dryland (0, 30, 60, and 120 Mg·ha⁻¹ wet weight) and irrigation (0, 60, 120, and 180 Mg·ha⁻¹) on SOC, SH, and SWR. In addition, we compared the effect of 44 yr of continuous annual manure applications (C44) to legacy treatments which had discontinued applications for 14 (D14) or 30 yr (D30). Laboratory measurements were conducted on air-dried and sieved (<2 mm) soil to determine SOC, SH using Fourier transform infrared spectroscopy, and SWR using the repellency index (RI) method. Mean RI values for all treatments ranged from 2.20 to 13.0, indicating subcritical (RI > 1.95) SWR. Manure application rate had a significant (P ≤ 0.05) and positive effect on SOC and SH, and both followed an exponential model. In contrast, RI had a negative response to the application rate under dryland and had no response under irrigation. Overall, positive responses of SOC and SH to application rate supported our hypothesis, but it was not supported for RI. The hypothesis of greater SOC, SH, and RI for continuous versus discontinued treatments was also supported for SOC and SH but not for RI.