Baseflow is among the most important components of streamflow. It is the main source of streamflow from groundwater systems in the dry season and also plays an important role as a water resource in the ecological environment and for human activities. In recent years, because of climate change, the number of dry season days in Taiwan has increased, and the wet season has been delayed, resulting in fewer rainy days and increased precipitation intensity. In addition, the spatial distribution of rainfall is uneven, and rivers are short and fast-flowing. Taiwan has become a country with abundant rainfall but insufficient water resources; therefore, the assessment of baseflow is important. This study selected eight basins with distinct wet and dry seasons in southern Taiwan as the study area. The baseflow characteristics and their relationships with climate features were assessed using time series analysis, baseflow attribution analysis, and wavelet analysis. The results showed that baseflow has an increasing trend; both precipitation and evapotranspiration have a significant positive correlation with baseflow, and the impact of precipitation is greater than that of evaporation. Sensitivity analysis showed that baseflow increases with increasing evaporation and precipitation; this behavior is related to the concentration of precipitation and evaporation in the wet season. Baseflow attribution analysis showed that the contribution of climate change to baseflow (75.0%) was larger than that of human activities (−2.9%), indicating that climate change was the main factor in the increase in baseflow. Wavelet analysis showed that both the El Niño–Southern Oscillation (ENSO) and Pacific Decadal Oscillation (PDO) are correlated with baseflow, where the PDO is more strongly correlated than the ENSO. The main timescales of the ENSO and PDO are a 4–8-year band and an 8-year band, respectively. The ENSO may have a timescale above the 8-year band, and the PDO exhibits periodic correlation changes at a 1-year band.