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Baseflow, a component of the total streamflow, plays a key role in maintaining aquatic habitats, particularly during extreme drought events. This study investigated baseflow response to a prolonged and extreme meteorological drought event in the Baiyangdian Basin (BYD basin), a temperate water-limited basin in North China. Applying a precipitation series, piecewise regression was used to determine this extreme meteorological drought event, while the Automatic Baseflow Identification Technique (ABIT) was used to estimate a recession parameter (α), which was used to isolate baseflow from total streamflow. Results showed that: 1) annual precipitation exhibited significant decreasing trends (P < 0.05) with an average change of −1.81 mm/yr2. The precipitation deficit revealed that the start and end date of the extreme meteorological drought event was from August 1996 to May 2011, respectively, persisting for a total of 178 months (roughly 15 yr); 2) hydrological drought (including streamflow and baseflow) lagged behind meteorological drought while predictably persisting longer than extreme meteorological drought (i.e., precipitation); and 3) baseflow decreased dramatically under meteorological drought at both seasonal and annual scales, resulting in significantly decreasing trends during drought periods. Findings from this study confirmed that hydrological events caused by extreme meteorological drought can alter the magnitude and duration of baseflow and total streamflow, which will have an inevitable influence on aquatic ecosystems.