The sediment transport capacity plays a pivotal role in erosion research, and is usually predicted using hydraulic variables. The transport capacity and hydraulic variables are affected by vegetation cover. Our understanding of the effect of vegetation cover, including the size, density, and arrangement of vegetation stems, on the relationship between the sediment transport capacity and hydraulic variables were rather limited. The objectives of this study were to investigate the effect vegetation stem cover on the relationship between hydraulic variables and the sediment transport capacity and to derive an equation for predicting the sediment transport capacity in the presence of vegetation cover. Five data sets from 288 flume experiments with a wide range of discharge (0.25–2 × 10−3 m3 s−1), slope (8.8–42.3%), median sediment diameter (0.11–1.16 × 10−3 m), stem cover (0–30%), stem diameter (2–36 mm), and stem arrangement (bead, tessellation, zigzag, random, and banding) were compiled for this study. Extensive regression analysis has shown that the sediment transport capacity could be expressed as a power function of flow velocity, shear stress, stream power, or unit stream power. Predictors of the sediment transport capacity were ranked from the unit stream power as the strongest, followed by the stream power, flow velocity, and the shear stress. Vegetation stem cover had no apparent and direct effect on the relationship between hydraulic variables and the sediment transport capacity so long as the unit stream power or stream power was used as its predictor. Vegetation cover became a significant factor only when the shear stress was used to predict the sediment transport capacity. Finally, a new equation involving the slope gradient, flow velocity, and median sediment diameter in a nondimensional form was shown to be a superior predictor of the sediment transport capacity with the Nash–Sutcliffe coefficient of efficiency of 0.92. The product of slope and flow velocity, that is, the unit stream power, captures the effect of vegetation stem cover and surface roughness and was shown to be an effective predictor of the transport capacity in the presence of vegetation cover.