Reconstructing fire regimes and fuel characteristics is an important aspect of understanding past forest ecosystem processes. Fuel sources and fire regimes in the upper Midwestern United States have been shown to be sensitive to regional climatic variability, such as drought periods on millennial timescales. Yet, records documenting the connections between disturbance activity and the corresponding fuel source fluctuations in mesic deciduous forests and prairie/oak savanna in this region are limited. Thus, it has been difficult to provide a framework to evaluate changes in moisture availability on fire activity and the relationships with fuel source fluctuations in this region. We present high-resolution charcoal analyses of lake sediments from four sites in southern Wisconsin (USA) to characterize fire activity and fuel source fluctuation in mesic deciduous forests and prairie/oak savanna over the last 10 000 years. We found that fire occurrence across the four study sites has been asynchronous throughout the Holocene, because of site-specific differences that have strongly influenced local fire regimes. Additionally, we found that during periods of high fire activity the primary fuels were from arboreal sources, and during periods of low fire activity the primary fuels were from non-arboreal sources. However, fluctuations in fuel sources did not always correspond to changes in vegetation, or changes in fire frequency.