The fluvial processes of sediment-laden flow running through the Xiaobeiganliu (XBGL) River reach changed dramatically after the year 2000. Thus, the connection between the sediment source area (area between Toudaoguai and Longmen) and the lower channel requires further analysis. This study aims to investigate the effects of human activities in the drainage area of Toudaoguai-Longmen on XBGL River reach and the Lower Yellow River (LYR). Prior to 1999, deposition in XBGL was positively correlated with inflow sediment and runoff entering the river reach. The correlation between these two variables became negative after 1999. The ratios between deposition in XBGL and change of runoff and sediment by human activities in the upper drainage area were 0 in 1971-1984, 0.15 in 1985-1998, and -0.39 in 1999-2012. For the changed deposition processes of the XBGL, the ratios between deposition in the LYR and change of runoff and sediment by human activities in the upper drainage area were 0.87 in 1971-1984, 0.92 in 1985-1998, and 2.33 in 1999-2012. The analyses revealed the important role of XBGL in sediment storage in the river system, where the decrease in inflow suspended sediment load of XBGL results in a likely increase in the outflow of the river reach.