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Agricultural, municipal, industrial, and environmental stakeholders began collaborating in 1990 to address water quality improvements in the Lower Boise River watershed. Preliminary analysis indicated that water quality concerns could be addressed through additional control of both point and nonpoint discharges in the watershed. It was also recognized that refinements in water quality standards were needed and new market-based tools (e.g., trading) would aid in implementing cost effective pollution reductions. Lower Boise River Water Quality Plan, Inc. was formed in 1994 to protect appropriate designated uses of the Boise River and to ensure that related expenditures provide real environmental benefits.

Idahos Total Maximum Daily Load (TMDL) lawsuit was filed in 1993 over listing of impaired waters. The State of Idaho (State) modified its 1992 list, more than doubling the number of impaired segments. The court found the revised list inadequate. The State adopted an 864 segment list, waterbody assessment methods, TMDL statutes creating Basin and Watershed Advisory Groups to develop TMDLs, and an 8-year TMDL development schedule in 1996.

Major accomplishments in the Lower Boise and Snake River-Hells Canyon watersheds include significantly improved understanding of pollution sources and routing and significant TMDL innovations (use and criteria refinement, phased/prioritized implementation, cost effective allocations, trading, realistic timeframes; allocation to unconventional sources). Specific accomplishments in the Lower Boise include: water quality data collection and reports; delisting 10 pollutants on four mainstem segments; approval of Sediment and Bacteria TMDLs; tiered/prioritized TMDL Implementation Plan; five tributary Use Attainability Analyses; Bacteria DNA Source Identification study; and a pollutant trading pilot project. Snake River Hells canyon accomplishments include: application the Lower Boise lessons learned in the Snake River-Hells Canyon TMDLs and assessment of uses and criteria;