Numerous oxbow lakes occur along the Brazos River, which stretches over 840 miles across Texas. Created by lateral stream erosion and changes in the course of the river, these lakes were formed when the main stream channels were abandoned. When the oxbow lakes and main channel connect during floods, the water from these surface water bodies mixes, resulting in an exchange of aquatic plant and animal species. These exchanges are important avenues for maintaining biodiversity in a river ecosystem. The main focus of this investigation was to determine the source water of three oxbow lakes near Bryan and Hempstead, Texas. Using site topography and water surface elevation information, we evaluated surface connections of each oxbow lake with the main channel of the river. We estimated recurrence intervals for connections based on historical streamflow and ground survey measurements. Results indicate that Moelhman Slough connects to the Brazos River at least twice per year, Korthauer Bottom connects to the Brazos River more than once per year, and Horseshoe Lake rarely connects to the Brazos River, even during intense flood events. We sampled the three oxbow lakes, river water near the lakes, adjacent groundwater from the shallow alluvial aquifer, and the Queen City, Sparta, and Evangeline aquifers that lie below the alluvium for isotopic and chemical compositions. Isotopic compositions of the alluvial groundwater, river water, and oxbow lake water show a progressive enrichment in oxygen and deuterium isotopes due to their continued evaporation. Groundwater in the alluvial aquifer shows unenriched isotopic values due to an absence of any significant evaporation during recharge. When groundwater from the alluvium discharges as base flow into the river, it mixes with the river water causing enrichment in isotopic values. In the oxbow lakes, higher evaporation occurs because water is locked into shallow, standing bodies of water, which leads to more enriched values. Groundwater from the Queen City, Sparta, and Evangeline aquifers near the lakes has more depleted isotopes and a sodium-bicarbonate composition that differentiates it from the more enriched isotope and calcium-sodium-bicarbonate composition of groundwater from the Brazos River Alluvium Aquifer. These differences in chemical and isotopic compositions suggest that there may not be any significant upward discharges from the Queen City, Sparta, and Evangeline aquifers into the Brazos River Alluvium Aquifer and the Brazos River. Water levels and base flow analyses suggest that a substantial portion of the water in the Brazos River is derived from base flow from the shallow alluvial aquifer. Estimated average base flow discharges are significantly higher downstream than upstream. Fresher (less saline) groundwater composition in the lower parts of the alluvial aquifer produces a fresher river water composition downstream. We estimated recharge into the Brazos River Alluvium Aquifer using base flow and chloride mass balance methods. Using the base flow method, we estimate that average recharge into the aquifer ranges from 0.74 to 0.95 inches per year. Using the chloride mass balance method, we estimate average recharge is about 0.33 inches per year; however, this method may underestimate recharge if chloride is derived from non-precipitation chloride. Water levels in wells and base flow discharges show no direct responses with precipitation amounts, suggesting that recharge into the aquifer is delayed due to the presence of clay in or above the alluvium, as documented by recent geophysical investigations. From a combined use of surface water connections, water chemistry, isotopic composition, and base flow amounts in different segments of the Brazos River, we suggest that the source water for Moehlman Slough and Korthauer Bottom differs from Horseshoe Lake. The frequency and duration of surface connections of the oxbow lakes with the river in combination with characteristic chemical and isotopic compositions suggest that the water in Moelhman Slough and Korthauer Bottom originated during flood events. In contrast, base flow from the alluvial aquifer is the dominant source of water for Horseshoe Lake. Water in Horseshoe Lake has experienced extensive evaporation, which is supported by its enriched deuterium and oxygen isotopic compositions and only one surface connection to the Brazos River over the past 20 years. Although chemical composition of the water from Horseshoe Lake should be more saline due to extensive evaporation, it remains surprisingly fresher than all other water. This difference in chemical composition could possibly be attributed to biologically mediated filtering of the ions and/or geochemical reactions.