The main aim of this paper was to analyze the sensitivity of the five infiltration equations (Kostiakov, Kostiakov–Lewis, Philip, Horton and SCS) and their coefficients to various ponding depths and initial soil moisture under different irrigation managements. The treatments included three qualities of water (electrical conductivity = 6, 3 and 0.6 dS/m), two managements of irrigation (intermittent irrigation and daily irrigation) and three irrigation periods (100, 45 and 8 days). The HYDRUS-1D model was calibrated to simulate infiltration in various initial soil moistures and ponding depths. Evaluating the performance of infiltration equations showed that the Horton and Kostiakov–Lewis had better accuracy and Kostiakov and SCS had less accuracy than the other equations. The empirical coefficients of SCS and Kostiakov had the most and least sensitivities, respectively. Furthermore, Horton was the most sensitive equation, while SCS was the least sensitive one. The output parameters under daily management were the most sensitive to variations in infiltration coefficients, especially when the salinity and sodium contents of water and soil were higher. The results also showed that the effect of the initial soil moisture on the infiltration coefficient in high permeable soil (arising from daily management) was greater; but in low permeable soil (arising from intermittent management), the ponding depth was more effective. It is concluded that the infiltration equations (specifically the SCS equation) and their coefficients (specifically coefficient c) should be calibrated relative to the initial soil moisture, ponding depth, soil solution and water irrigation quality. Particularly in areas with high permeable soil (in the daily management), the calibration of the infiltration equation should be conducted with the initial soil moisture. In these areas, the irrigation period should be controlled. In areas with low permeable soil (in intermittent management), calibration should be carried out relative to the ponding depth. In these areas, the inflow rate should be controlled.