Stream ecosystems and their riparian ecotones are among the most important and most threatened natural resource areas in the Pacific Northwest. Military installations in the region often contain valuable aquatic habitat that supports several threatened or endangered species of salmonids. These sensitive areas need to be properly managed under the Endangered Species Act, while supporting military operational capability within their watersheds.  

The overall goal of this SERDP Exploratory Development (SEED) project was to determine a suite of ecological-based indicators for stream and wetland ecosystems. Indicators are needed to measure environmental change resulting from a shift in the natural disturbance regime due to the cumulative effects of watershed urbanization in general and military operations in particular. A management framework was developed for stream ecosystem protection and restoration based on active management for natural ecological integrity.

Technical Approach

This project investigated a range of physical, chemical, and biological parameters that could be used as tools for assessing changes in natural ecosystem structure and function resulting from military activities within the study watersheds. Military operations impacting aquatic resources were identified and quantified early in the project, and sites were selected for detailed reach-level field surveys. These detailed surveys included riparian corridor characterization, chemical water quality monitoring, instream habitat surveys, hydrologic monitoring, geomorphic surveys, and biological monitoring (salmonids and benthic macroinvertebrates). Natural reference sites also were identified and quantified as the basis for establishing restoration/rehabilitation target conditions. Data were analyzed to identify relationships between military operations, watershed conditions, potential measures of ecological integrity, and salmonid population indicators such as spawning counts and juvenile abundance estimates.


The results of the habitat assessments indicate that channel and habitat structure of a number of the segments in most streams are frequently degraded relative to values from published “properly functioning conditions” for the Puget Sound or the Pacific Northwest region. For example, bankfull width to depth ratios are often larger than prescribed properly functioning conditions ratios, suggesting that channel dynamics are unstable. Pool habitat frequencies are lower than standards and of low quality in most segments. This decreased slow water “rearing” habitat may limit juvenile carrying capacity as well as hinder upstream migration by adult salmon. In addition, instream habitat complexity and large woody debris (LWD) abundance and quality are significantly degraded, exacerbating rearing habitat deficiencies and compounding the hydro-geomorphic instability. The low amounts of instream LWD may be partially responsible for the low pool frequency. LWD frequency was closely related to pool frequency in most study streams as it is in undisturbed streams of the Pacific Northwest.

These data suggest that processes creating natural habitat structure may be changed from natural conditions. Analysis of basin land cover reveals less forested and increasingly impervious cover, as well as a significant loss of wetlands, which has been shown to alter the basin hydrologic regime. This change in basin hydrology leads to destabilization of channel morphology. Riparian vegetation also seldom resembled natural conditions and was nearly completely depleted of sources of high quality, coniferous LWD. Dominant riparian vegetation often included landscaping, invasives, and young deciduous forest.


Results of this project provide military installations in the Pacific Northwest with tools to better manage aquatic resources. A regional database relating the degree of watershed disturbance and ecological integrity to salmonid utilization, including abundance of species composition and instream habitat quantity and quality, was generated. In addition, protocols were developed for measuring the physical, chemical, and biological components of stream ecological integrity. These protocols will help military natural resource managers work more cooperatively with non-military jurisdictions and regulatory agencies on issues of salmonid resource management.