The interaction between groundwater and surface water in northern Shaanxi is quite complicated and frequent under the influence of regional hydrogeological condition and human intervention. These performances bring serious challenges to regional water resources assessment and utilization. The river baseflow process at Gaojiabu Station in windy desert region, Gaoshiya and Caoping Station in loess region were taken as research objects, and their variation trends and change points in the river baseflow series were analyzed in this paper. In addition, to explore the cause of the baseflow change, this research compared their correlations with precipitations in the same area respectively from two aspects of flow variation and multitimescale characteristics. The results show that: ①groundwater recharges for river flow in windy desert region significantly exceed those in loess region; ②baseflows of all the rivers in the study area reducing significantly are mainly determined by human intervention such as the extensive pumping of groundwater; ③periodic changes of baseflow in each station response closely to precipitation change on meso-scale and small-scales; ④precipitation-runoff relationships in windy desert regions are much more complicated and unstable than loess region, which is mainly because of its more significant impact from groundwater storage and the lateral recharge change. Under the changing environment, the water cycle in windy desert regions would be in complexity and variability. Therefore, it is recommended that, groundwater changes need to be considered in regional water resources assessment.