Primarily located in the state of Montana, the 320-mile long Clark Fork River flows from near Butte, Montana to Lake Pend Oreille in Idaho. This document addresses the lower-most 247 square miles of the subbasin located in north Idaho. The Lower Clark Fork River provides over 92% of the inflow to Lake Pend Oreille, the recreational and economic hub of the area.

The Lightning Creek watershed harbors a regionally significant bull trout population and supports many other native fish. Both the mainstem Lower Clark Fork River and Lightning Creek are designated Special Resource Waters by the state of Idaho. Special protections of beneficial uses in these waters are given in recognition of their outstanding or unique characteristics.  Primarily, this designation prohibits additional point source pollution permits to protect current beneficial uses.

Metals and total dissolved gas pollution are the pollutants of concern in the mainstem Clark Fork River. Intensive mining around the headwaters of the Clark Fork River in Montana left residues of heavy metals behind, which still pose a risk to water quality throughout the basin.

Temperature is identified as a pollutant in the Lower Clark Fork River below the Idaho/Montana border. However, the Lower Clark Fork River on the Montana side of the border has not been found to violate Montana water quality standards for temperature. To better address this issue at a watershed level, Idaho and Montana will investigate available information before the five-year review of this TMDL.  Temperature will remain in Section 5 of Idaho's Integrated Report until this time.

Sediment and temperature are the pollutants of concern in the tributaries to the Lower Clark Fork River. Thick glacial outwash sediments in steep drainages combined with timber harvest and road construction have created potential sediment problems in several of the tributaries to the Clark Fork River. Temperatures exceed Water Quality Standards for salmonid spawning throughout the subbasin. Fire and historic timber harvest have created a more open canopy and related stream warming compared to background conditions.

TMDLs were developed for each stream determined to not fully support beneficial uses in accordance with state of Idaho Water Quality Standards. The TMDLs included in this document address in-stream sediment, metal, and temperature reduction goals to maintain or restore cold water aquatic life and salmonid spawning in the
tributaries. Cadmium, zinc, copper, and total dissolved gas TMDLs were developed for the main stem Clark Fork River. Sediment and temperature TMDLs were developed in the Lightning Creek drainage and for Twin and Johnson Creeks. The TMDLs help quantify needed improvements and target management actions to address water quality improvement measures and timelines.