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We describe a protocol to monitor the effectiveness of the Tongass Land Management Plan (TLMP) management standards for maintaining fish habitat. The protocol uses juvenile coho salmon (Oncorhynchus kisutch) in small tributary streams in forested watersheds. We used a 3-year pilot study to develop detailed methods to estimate juvenile salmonid populations, measure habitat, and quantitatively determine trends in juvenile coho salmon abundance over 10 years. Coho salmon have been shown to be sensitive to habitat alterations, and we use coho salmon parr as the primary indicator in the protocol. A priori criteria for type I and type II error rates, effect size, and sample sizes for the protocol were derived with estimates of variance computed from the 3-year pilot study. The protocol is designed to detect trends in abundance of coho salmon parr, as well as coho salmon fry and Dolly Varden (Salvelinus malma), in small streams managed according to TLMP standards and guidelines and to compare these to trends in unmanaged (old-growth) watersheds. Trends are adjusted to account for statistically significant habitat covariates. This information provides an important element in monitoring land management practices in the Tongass National Forest. The methods we describe may have application to monitoring protocols elsewhere for fish populations and land management practices.