In 1996 the Wyoming Department of Environmental Quality (WDEQ) listed Prairie Dog Creek on the 303 (d) list of impaired water bodies.  This was due mainly to the concentrations of manganese and other contaminants within the stream..  Consequently, the WDEQ included Prairie Dog Creek into the "Beneficial Use Reconnaissance Program" (BURP) for additional monitoring.  Results of the BURP assessment and subsequent water quality sampling data initially removed Prairie Dog Creek from the 303 (d) list and placed it on WDEQ's "Needs to be Monitored" list.

Monitoring continued, and in 2002 Prairie Dog Creek was re-listed and placed in Table A of Wyoming's 303 (d) List of Waters Requiring Total Maximum Daily Loads (TMDLs) for drinking water impairments.  This was due primarily to elevated manganese concentrations.  This listing came as a result of monitoring done by the United States Geological Survey (USGS) at Station Number 06306250 and was assigned a low priority for TMDL development (WDEQ, 2002).  While the concentrations indicated impairments for aesthetic drinking water use (discoloration), the manganese concentrations were not believed to pose a human health risk (WDEQ, 2002).  In 2004, the entire Prairie Dog Creek watershed was placed on the 303 (d) List for fecal coliform impairments related to recreational uses.  This came as a result of WDEQ monitoring in July 2003 (WDEQ, 2003) and was assigned a high priority for TMDL development because no local group had committed to develop a watershed plan (WDEQ, 2004b).  In 2004 SCCD was denied 319 funding to initiate an assessment and planning effort on Prairie Dog Creek.  SCCD addressed the concerns of the non-point source task force and reapplied for funding in 2005.  In August 2005, additional sampling by WDEQ (WDEQ, 2005), indicated significant bacteria concerns on water bodies in the unincorporated town of Story, Wyoming.  Story lies adjacent to the watershed and is an integral hydrological part of the Prairie Dog Creek watershed.  A large quantity of the water in Prairie Dog Creek originates from trans-basin diversions from the Piney Creek drainage in and around Story.

As a result of the previous water quality monitoring in the Prairie Dog Creek watershed, there are indications that recreational uses are not being achieved due to elevated concentrations of bacteria (WDEQ, 2003).  These previous monitoring efforts were sufficient to identify Prairie Dog Creek as impaired; however, they were insufficient in both frequency and duration to establish representative baseline watershed conditions required to initiate an effective local watershed planning effort.  In the spring of 2007, SCCD began a two-year watershed assessment to provide adequate baseline water quality data, which is necessary to provide information to stakeholders for the development and implementation of the Prairie Dog Creek Watershed plan.  Further, data from this monitoring assessment will allow the examination of long-term trends in water quality improvement that may result from the Prairie Dog Creek watershed plan.  SCCD finished up it first year of monitoring in the fall of 2007 and is set to do the consecutive year of monitoring beginning in April of 2008.