Recent rulings of the U.S. Supreme Court have limited Clean Water Act jurisdiction over actions affecting isolated wetlands and intermittent or ephemeral streams. In a semi-arid environment like Montana, isolated wetlands and impermanent streams are often critical refugia, breeding areas, or food sources for wildlife, and harbor many plant species that could not survive in the surrounding uplands. The purpose of this project was to conduct GIS-based analysis to assist the Montana Department of Environmental Quality in assessing the distribution and extent of the resources affected, including the ecological functions and values they represent. We used a series of data processing routines and subroutines to identify geographically isolated wetlands. For the purpose of the analysis, we defined geographically isolated wetlands as those palustrine wetlands that met all the following tests: 1) not on a large river floodplain, defined as a 300 meter buffer on either side of the river; 2) more than 40 meters from any perennial or intermittent stream or river, whether or not that stream or river was a tributary of a navigable river; 3) not connected to a wetland that was itself on a large river floodplain or within 40 meters of a perennial stream or river; 4) not within 40 meters of a large (>20 acre) lake or wetland with a perennial stream inflow or outflow; and 5) more than 20 meters from any ephemeral channel. We also used a similar approach to identify wetlands that were likely to fall within Clean Water Act jurisdiction, wetlands that might meet a "significant nexus" test to establish jurisdiction, and wetlands whose classification could not be determined from a GIS. To identify impermanent streams, we used both medium-resolution and high-resolution hydrography data to categorize all streams represented on 1:24,000 topographical maps into perennial, intermittent and ephemeral categories. Finally, we assigned landscape position, landform, water regime and water path attributes to the isolated wetlands we identified, and used these as the basis for rating each isolated wetland type's average performance expectation on each of ten wetland functions. The analysis showed that of 252,186 natural wetlands currently mapped in Montana, 152,726 -- 61% of all mapped wetlands -- have no visible surface water connection to any other water body. When only palustrine wetlands are considered, 65% of wetlands across the statewide mapped areas are isolated. Palustrine emergent wetlands account for 91% of isolated wetlands. These wetlands characteristically have a short inundation period; 93% have either a seasonally flooded or a temporarily flooded water regime. In terms of wetland acreage, the percentages are lower, simply because geographically isolated wetlands are typically small (less than half the average size of palustrine wetlands). Mapped wetlands in Montana cover some 735,338 acres; of this total, 176,224 acres are geographically isolated. Even in the Northwestern Glaciated Plains, where 50% of palustrine wetlands are geographically isolated, only 30% of the total palustrine acreage is isolated. By contrast, only 19,314 mapped wetlands in Montana -- less than 8% of the total -- are associated with navigable rivers or large lakes or have a continuous surface water connection to other large rivers. These wetlands are likely to meet the threshold required for an assertion of jurisdiction by the Army Corps of Engineers or the EPA. We identified an additional 31,196 wetlands -- almost 13% of all mapped natural wetlands -- that were most likely to have a "significant nexus" to a navigable river or its tributaries, and an additional 327 wetlands that were near large wetlands connected to perennial rivers. The remaining 20% could not be classified using GIS alone. Our analysis of streams revealed that on a statewide basis, ephemeral and intermittent streams far outnumber perennial ones. In some ecological subsections within the Northwestern Glaciated Plains and Northwestern Great Plains, there were no perennial streams at all. Only in the Canadian Rockies did we find that there were more kilometers of perennial stream than intermittent and ephemeral.