Increased use of streamflow, most importantly minimum flow/baseflow data should be incorporated into drought indices, especially in regions where streams have a high baseflow component. Standard departure for streamflow (SDSF) and standard departure for baseflow (SDBF) were compared to the standardized precipitation and evapotranspiration index (SPEI) drought index values for 17 baseflow-dominated watersheds in the northern, central, and southern regions of Wisconsin. For each watershed, comparisons of SDSF, SDBF, and SPEI time series (for 1, 3, and 12-month time scales) were evaluated using correlation, run lengths of negative and positive values, sign congruence, and Mann-Kendall trend test. In general, SDBF performed better than SDSF for longer time scales. Trends of wetness appear to be distinguished earlier in SDBF compared to SDSF and SPEI-1, SPEI-3, and SPEI-12. The results of this study are consistent with regional statewide climate studies on precipitation and changes in precipitation intensity. This study highlights how standardized baseflow data are robust and compare to SPEI 12-month time scales.