Cement channel linings in an urban stream in St. Louis, Missouri increase event water contributions during flooding, shorten transport times, and magnify geochemical variability on both short and seasonal timescales due to disruption of hyporheic flowpaths. Detailed analyses of water isotopes, major and trace elements, and in situ water quality data for an individual flood event reveal that baseflow contributions rise by 8% only 320 m downstream of the point where this particular channel changes from cement-lined to unlined. However, additional hydrograph separations indicate baseflow contributions are variable and can be much higher(average baseflow increase is 16%). Stream electrical conductivity(EC) and solute concentrations in the lined reach were up to 25% lower during peak flow than in the unlined channel, indicating a greater event flow fraction. In contrast, during low flow, stream EC and solute concentrations in the lined reach were up to 30% higher due to the restricted inflow of more dilute groundwater. Over longer timescales, EC, solute concentrations, turbidity, and bacterial loads decrease downstream signifying increasing contributions of dilute baseflow. The decreased connectivity of surface waters and groundwaters along the hyporheic zone in lined channels increases the hydrologic and geochemical variability of urban streams. Cement channel linings in an urban stream in St. Louis, Missouri increase event water contributions during flooding, shorten transport times, and magnify geochemical variability on both short and seasonal timescales due to disruption of hyporheic flow path. Detailed analyzes of water isotopes, major and trace elements, and in situ water quality data for an individual flood event reveal that baseflow contributions rise by 8% only 320 m downstream of the point where this particular channel changes from cement-lined to unlined. However, additional hydrograph separations indicate baseflow contributions are variable Stream electrical conductivity (EC) and solute concentrations in the lined reach were up to 25% lower during peak flow than in the unlined channel, indicating a greater event flow fraction. In contrast, during low flow, stream EC and solute concentrations in the lined reach were up to 30% higher due to the restricted inflo Over decreased timescales, EC, solute concentrations, turbidity, and bacterial loads decrease downstream signifying increasing contributions of dilute baseflow. The decreased connectivity of surface waters and groundwaters along the hyporheic zone in lined channels increases the hydrologic and geochemical variability of urban streams.