The lower coastal plain of the Southeast USA is undergoing rapid urbanisation as a result of population growth. Land use change has been shown to affect watershed hydrology by altering stream flow and, ultimately, impairing water quality and ecologic health. However, because few long-term studies have focused on groundwater–surface water interactions in lowland watersheds, it is difficult to establish what the effect of development might be in the coastal plain region. The objective of this study was to use an innovative improvement to end-member mixing analysis (EMMA) to identify time sequences of hydrologic processes affecting storm flow. Hydrologic and major ion chemical data from groundwater, soil water, precipitation and stream sites were collected over a 2-year period at a watershed located in USDA Forest Service's Santee Experimental Forest near Charleston, South Carolina, USA. Stream flow was ephemeral and highly dependent on evapotranspiration rates and rainfall amount and intensity. Hydrograph separation for a series of storm events using EMMA allowed us to identify precipitation, riparian groundwater and streambed groundwater as main sources to stream flow, although source contribution varied as a function of antecedent soil moisture condition. Precipitation, as runoff, dominated stream flow during all storm events while riparian and streambed groundwater contributions varied and were mainly dependent on antecedent soil moisture condition. Sensitivity analyses examined the influence of 10% and 50% increases in analyte concentration on EMMA calculations and found that contribution estimates were very sensitive to changes in chemistry. This study has implications on the type of methodology used in traditional forms of EMMA research, particularly in the recognition and use of median end-member water chemistry in hydrograph separation techniques. Potential effects of urban development on important hydrologic processes (groundwater recharge, interflow, runoff, etc.) that influence stream flow in these lowland watersheds were qualitatively examined. Copyright © 2011 John Wiley & Sons, Ltd.