We evaluated the status of remnant prairie patches in the Loess Hills of southeastern South Dakota using three parallel approaches. Aerial photograph analysis, vegetation surveys and stable carbon isotope analysis of soil organic matter all yielded evidence of woody plant encroachment. Time series analysis of aerial photos indicated that forest cover expanded by 37.5% between 1941 and 2000. Vegetation surveys revealed several distinct community types ranging from forested ravines supporting basswood, American elm and black walnut trees to upland prairie remnants and oak savannas that now include encroaching eastern red cedar trees, and/or a dense understory of prickly ash, ironwood and other woodland species moving up from the ravines. Finally, carbon isotope values (δ¹³C) in soil cores decreased as much as 5–7‰ towards the soil surface consistent with increased prevalence of C₃ forest species over C₄ prairie species in recent years. One consequence of forest encroachment appears to be an increase of 35% in soil organic carbon (SOC) content in surface soils. At the current rate of encroachment and unless management techniques are employed to keep the forests in check as fires once did, we expect the existing prairie remnants to be completely replaced by forest within the next several decades.