We examined the impacts of changes in land cover and soil conditions on the flow regime of the upper Delaware River Basin using the Water Availability Tool for Environmental Resources (WATER). We simulated flows for two periods, circa 1600 and 1940, at three sites using the same temperature and precipitation conditions: the East Branch (EB), West Branch (WB), and mainstem Delaware River at Callicoon, NY. The 1600 period represented pristine forest and soils. The 1940 period included reduced forest cover, increased agriculture, and degraded soils with reduced soil macropore fractions. A model-sensitivity test examined the impact of soil macropore and land cover change separately. We assessed changes in flow regimes between the 1600 and 1940 periods using a variety of flow statistics, including established ecological limits of hydrologic alteration (ELOHA) thresholds. Reduced forest soil macropore fraction significantly reduced summer and fall base flows. The 1940 period had significantly lower Q50 flows (50% exceedance) than the 1600 period, as well as summer and fall Q90 and Q75-90 flows below the ELOHA thresholds. The 1- to 7-day minimum flows were also lower for the 1940 period, by 17% on the mainstem. 1940 flows were 6% more likely than the 1600 period to fall below the low-flow threshold for federally endangered dwarf wedgemussel (Alasmidonta heterodon) habitat. In contrast, the 1940 period had higher flows than the 1600 period from late fall to early winter.