IWRB implemented the Idaho Water Transactions Program (IWTP) in 2003 as a Qualified Local Entity of the Columbia Basin Water Transactions Program (CBWTP). The CBWTP was started in 2002 to support innovative, voluntary, grassroots strategies that improve flows to streams and rivers in the Columbia Basin.

The CBWTP is managed by the National Fish and Wildlife Foundation (NFWF), a not-for-profit organization dedicated to the conservation of fish and wildlife working in partnership with the Bonneville Power Administration (BPA). The majority of funding is provided by BPA in cooperation with the Northwest Power and Conservation Council (NPCC).

IWRB also used Pacific Coast Salmon Recovery Fund grants to leverage the money received through the CBWTP. In 2008, the State of Idaho signed the Idaho Fish Accord with BPA which established (in part) the Idaho Water Transactions Fund to provide $7.6 million over 10 years to fund water transactions in the Lemhi and Pahsimeroi River basins.