Vegetation cover can effectively prevent soil erosion and plays an important role in soil and water conservation. Accurate estimation of the sediment transport capacity (Tc) is critical for soil erosion models. Tc data for different levels of vegetation cover, however, are quite limited. The objectives of this study were to evaluate the influence of stem basal cover, slope gradient and discharge on the transport capacity of overland flows for Tc prediction. A non-erodible flume (5 m long and 0.37 m wide) was used in this study. The discharge ranged from 0.5 × 10−3 to 2 × 10−3 m3 s−1, the slope gradient was from 8.8% to 25.9% and an artificial stem basal cover of 0, 1.25%, 2.5%, 5%, 10%, 15%, 20%, 25% and 30% was used to represent the natural vegetation. Stems 2 mm in diameter were randomly arranged. The sediment size for the experiment ranged from 0.25 to 0.59 mm with a median diameter of 0.35 mm. The results show that the measured Tc decreased exponentially as the stem basal cover increased, and the rate of decrease was far greater than what has been reported in the literature. The transport capacity was affected more by the stem basal cover than by slope and discharge when the cover exceeded approximately 2–3%. The research shows that the surface or stem basal cover plays a critical role in reducing the transport capacity of overland flows.