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Understanding the link between terrestrial and aquatic systems is important because disturbance to terrestrial systems may also influence stream processes. Military training lands provide a unique opportunity to examine the influence of large-scale disturbance on terrestrial and aquatic communities in the absence of other anthropogenic disturbances (e.g., agriculture, urbanization). The objective of this study was to determine the effects of past mechanized infantry training on terrestrial and aquatic ecosystem properties on Fort Riley Military Reservation in northeastern Kansas. We used a long-term data set and supplemental study plots to determine the effects of military training use on terrestrial systems. Headwater and middle stream reaches were also sampled to determine the effects. of watershed training use on habitat and fish community structure. High military training use was associated with increased bare soil, reduced total plant cover, and compositional shifts in plant communities. Reduced cover of perennial, matrix-forming grasses and native species, and increased cover of annuals and introduced species were also associated with high training activity. High military training use in study watersheds was associated with increased sediment in pools and riffles and reduced abundance of benthic insectivores, herbivore-detritivores, and silt-intolerant species. Sites in-watersheds receiving high training use were also characterized by an abundance of trophic generalists and tolerant species. Our results suggest that military training activities,had significant ecological effects on the properties of terrestrial and aquatic ecosystems, both with respect to recovery from past disturbance and resilience to future disturbance.