Department of Defense (DOD) installation commanders and natural resource managers are tasked with providing an unimpaired training environment for troops while maintaining environmental integrity. In order for installations to achieve this balance, DOD has adopted the ecosystem-level management approach that relies on adaptive management of installation resources. An important and necessary component of adaptive management is long-term monitoring. However, identifying the appropriate metrics for longterm monitoring is a challenge. Streams are good candidates because they integrate impacts to the biotic, chemical, and physical components of a watershed and thus represent watershed integrity. One method for assessing stream quality is rapid bioassessment protocols (RBPs). The U.S. Environmental Protection Agency advocates use of RBPs for several applications including long-term monitoring. Most states and several tribes have adopted biomonitoring as part of their water quality programs. Examples of RBP programs in four southeastern states are discussed here. Because RBPs are utilized at the state and federal levels, they are appropriate candidates for DOD installations. In conclusion, RBPs are promising tools for long-term monitoring programs that are associated with adaptive management of DOD installations. © 2005 Wiley Periodicals, Inc.