The Hailiutu River basin is a typical area of semi-arid sandy land with relatively flat topography, the surface of which is covered by undulating dunes and the development of the river system is not obvious. The dominant hydrological cycle is precipitation infiltration through dunes to aquifers followed by discharge to rivers. Therefore, the baseflow is an important component of the streamflow in this basin, but few studies for the baseflow characteristics have been conducted. The isotope tracer technique was applied to investigate the contributions of groundwater, soil water, and surface water to streamflow during the flood period. The results showed that the contributions of these components to streamflow were approximately 70%, 27%, and 3% respectively. Several automatic baseflow separation methods including filtering and recursive digital filtering (RDF) techniques were adopted to separate the baseflow from the streamflow and the adaptabilities of these methods were evaluated. All the filtering methods including Hydrograph Separation Program (HYSEP) and UK Institute of Hydrology’s method (UKIH) clearly underestimated the baseflow when compared with the standard baseflow results which were provided by the previous study using the tracer-based method in this basin, while the recursive digital filtering with Eckhardt filter technique (RDF-E) produced better performance. In the nonprecipitation period, the RDF-E method misidentified quick flow values which caused deviations between the separated baseflow and the above standard value. Hence, we proposed a modified automatic baseflow separation method called RDF-M by introducing the precipitation information into RDF-E. In comparison with the above standard, the RDF-M method provided similar baseflow results which were consistent with the actual situation of the Hailiutu River basin.