Groundwater is managed by the Colorado Division of Water Resources. Permits are issued through the Denver office. You can get more information from the division's website. They also have a groundwater information line at 303-866-3587. Also, see the Colorado guide (PDF) to well permits, water rights and water administration.
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Please visit the EPA Surf Your Watershed for more information on the Roaring Fork Watershed. The Roaring Fork Conservancy can also answer many of your Roaring Fork Watershed questions
Obtaining water rights in Colorado is a complicated process and the rights to most of the water in Colorado are already held.
For a good general overview of what is involved in obtaining water rights, associated fees, and contact information for regional water courts in Colorado see the Colorado Division of Water Resource's water rights information.