Baseflow plays an important role in maintaining streamflow. Seventeen gauged watersheds and their characteristics were used to develop regression models for annual baseflow and baseflow index (BFI) estimation in Michigan. Baseflow was estimated from daily streamflow records using the two-parameter recursive digital filter method for baseflow separation of the Web-based Hydrograph Analysis Tool (WHAT) program. Three equations (two for annual baseflow and one for BFI estimation) were developed and validated. Results indicated that observed average annual baseflow ranged from 162 to 345 mm, and BFI varied from 0.45 to 0.80 during 1967–2011. The average BFI value during the study period was 0.71, suggesting that about 70% of long-term streamflow in the studied watersheds were likely supported by baseflow. The regression models estimated baseflow and BFI with relative errors (RE) varying from −29% to 48% and from −14% to 19%, respectively. In absence of reliable information to determine groundwater discharge in streams and rivers, these equations can be used to estimate BFI and annual baseflow in Michigan.