Manning’s roughness coefficient is one of the most important parameters in the design and evaluation of surface irrigation. In this study, Manning’s roughness coefficient was evaluated under two different inflow discharges (i.e., 0.29 and 0.44 L s− 1) on vegetated furrow irrigation during maize growing season. In addition, the accuracy of multilevel optimization and SIPAR-ID methods was evaluated for the estimation of Manning’s roughness coefficient and infiltration equation parameters in vegetated furrows. Spacing, length, and longitudinal slope of experimental furrows were 0.75 m, 110 m, and 1.2%, respectively. Values of the Manning’s roughness coefficient in the vegetated furrows increased as compared to its recommended values in bare furrows. On the contrary, inflow discharge had a weak inverse impact on Manning’s roughness coefficient. Roughness coefficient was the highest at downstream section (end) of the experimental furrow and its value at the middle section was higher than that of upstream section. The results also indicated that the multilevel optimization method had a good performance with average relative error (RE) about 5% for both discharges and SIPAR-ID method had an approximately proper estimation with relative error ranging from 4.6 to 15% in estimating Manning’s roughness coefficient for all irrigation events. To estimate the infiltrated volume of water into soil, the multilevel optimization method had a very good performance (RE = − 1.65 to 2.81%).