Infiltration and channel roughness, two major factors that govern stream discharge were studied between ephemeral streams (ES) and similar-sized perennial streams (PS) for two ephemeral flow conditions: with surface flow (wet season) and with ceased flow (dry season). The highest infiltration was observed at the low flow areas around the thalweg of ES in the dry season. Also, the infiltration in the high flow areas close to the channel margin was higher in ES than PS in the wet season but was similar in the dry season. Similar infiltration rates in ES and PS were rather unexpected and was attributed to the vegetation mat formed by air-dried litter because of the rapid decrease in sediment moisture. In high flow areas of both stream types in the wet season, negative and positive correlations were observed for infiltration with biomass and sediment organic content, respectively. Also, in a few cases sediment moisture showed a positive correlation with infiltration. ES were two to three times rougher than PS and standing crop biomass and/or litter content increased stream roughness and decreased with herb diversity. Impact of vegetation parameters on roughness was more prominent in PS, whereas mean particle size had equally strong importance on roughness for both streams other than perennials in the dry season. Modelled (via HEC-HMS) and observed discharges had a better agreement for PS. The field observations, analytical solutions as well as hydrological modelling revealed ES to have a lower unit discharge than PS.