During 2006–07, the U.S. Geological Survey (USGS), in cooperation with the Texas Water Development Board, did a study to quantify historical (water years 1966–2005) base flow and streamflow gains and losses from two streamflow-measuring surveys (March and August 2006) in the Brazos River from McLennan County to Fort Bend County, Texas. The Brazos River is hydraulically connected to the Brazos River alluvium aquifer, which in turn is hydraulically connected to several underlying aquifers, the outcrops of which occur in laterally adjacent layers generally parallel to the coast (major aquifers, Carrizo-Wilcox and Gulf Coast, and minor aquifers, Queen City, Sparta, and Yegua-Jackson). Hydrograph separation was done using the USGS computer program Hydrograph Separation and Analysis with historical streamflow from 10 USGS gaging stations, three on the Brazos River and seven on selected tributaries to the Brazos River. Streamflow data for computation of gains and losses were collected in March 2006 from 36 sites on the Brazos River and 19 sites on 19 tributaries to the Brazos River; and in August 2006 from 28 sites on the Brazos River and 16 sites on tributaries. Hydrograph separation and associated analyses indicate an appreciable increase in base flow as a percentage of streamflow in the reach of the Brazos River that crosses the outcrops of the Carrizo-Wilcox, Queen City, Sparta, and Yegua-Jackson aquifers compared to that in the adjacent upstream reach (on average from about 43 percent to about 60 percent). No increase in base flow as a percentage of streamflow in the reach of the Brazos River crossing the Gulf Coast aquifer compared to that in the adjacent upstream reach was indicated. Streamflow gains and losses computed for March 2006 for 35 reaches defined by pairs of sites on the Brazos River indicated that five reaches were verifiably gaining streamflow (computed gain exceeded potential flow measurement error) and none were verifiably losing streamflow. Four of the five gaining reaches are in the outcrop areas of the Carrizo-Wilcox and Yegua-Jackson aquifers. The results of the synoptic gain and loss surveys are consistent with the results of the base-flow analysis of historical streamflow. Appreciable increases in streamflow, apparently the result of increases in base flow, occur in the reach of the Brazos River that crosses the outcrops of the Carrizo-Wilcox, Queen City, Sparta, and Yegua-Jackson aquifers.