Streams in semi‐arid urban and agricultural environments are often heavily diverted for anthropogenic purposes. However, they simultaneously receive substantial inflows from a variety of ungaged sources including stormwater returns, tile drainage, and irrigation runoff that help sustain flow during dry periods. Due to the inability to identify sources or directly gage many of these inflows, there is a clear need for methods to understand source origination while quantifying potential gains and losses over highly impacted reaches. In the context of the Logan River Observatory, historical gage data illustrate the importance of ungaged and unidentified inflows on maintaining or enhancing flows in both urban and agricultural reaches containing large diversions. To understand the inflows in this portion of the Logan River, we first analysed water samples for ions collected from a subset of representative inflow sources and applied clustering analyses to establish inflow source classifications and associated ion concentration ranges. These representative concentration ranges, combined with mainstem flow and river ion samples taken at sub‐reach scales, allow for the application of flow and mass balances to quantify inflow rates from different sources as well as any losses. These calculations demonstrate significant gains and losses occurring in many sub‐reaches during three sampling events. The dominant land use (urban or agriculture) and flow regime at the time of sampling were the primary drivers of gains and losses. These exchanges were found to be most important below large diversions during low flow conditions. This highlights the need to classify inflow sources (urban or agriculture, surface or groundwater) and estimate their contributions to anticipate instream consequences of land use and water management decisions. As irrigation and water conveyance practices become more efficient, a portion of these ungaged inflows could be diminished or eliminated, thus further depleting streamflow during dry periods.