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Since time immemorial, indigenous people have relied on the streams of their territory for food, fiber, transportation, recreation, cultural, and spiritual needs. Accordingly, tribal people-particularly those in the region now called the Northwestern United States-placed singular emphasis on preserving their traditional subsistence culture when negotiating with the United States during the reservation era. Although rarely expressed in these treaties, the tribes are nonetheless entitled to water rights sufficient to fulfill these traditional subsistence treaty rights. Of the suite of water rights to maintain traditional uses of water, likely the most commonly claimed is for water to maintain fish habitat. A companion article in this same issue explores the evolution of the methodology for quantifying these water rights, which has slowly converged on the Instream Flow Incremental Methodology (IFIM) and its component part, the Physical Habitat Simulation Model (PHABSIM) methodology. The purpose of this Article is to provide an explanation of the current IFIM/PHABSIM methodology to put practitioners in the position to understand and meaningfully apply the method.