Between 1989 and 1994, Brown Nicollet Cottonwood Environmental Health monitored the upper reaches of the watershed as part of a groundwater study in the three counties. Results indicated that groundwater and surface water were connected and that poor quality surface water was probably contributing to the poor quality of groundwater in this area.
In spring 1996, The U. S. Geological Survey intensified its monitoring of the watershed as part of the Middle/Lower Minnesota Assessment Project to identify which surface waters were negatively affecting the Minnesota River.

In 1997, the Minnesota Pollution Control Agency granted a Clean Water Partnership (CWP) to the Brown Nicollet Cottonwood Water Board (Board) to study the watershed further. Soon after, four water-quality monitoring stations were established in the watershed. Due to a tornado that struck parts of the watershed in the spring of 1998, the project was put on hold for one year.

Results from the study (1997-2000) indicated that reductions in sediment, nitrates, and phosphorus throughout the watershed would improve water quality in the main stems of the Little Cottonwood and Minnesota Rivers. However, although water quality was a concern, flooding was found to be a bigger problem for the watershed. The technical committee identified several actions that would help not only lower the non-point sources of pollution in the watershed but also remediate problems from flooding.

In 2001, the project received implementation-phase funding from the CWP program to accelerate the adoption of voluntary practices by landowners to restore the watershed. The watershed project began to work with landowners and farmers to help them make their property and land use practices "watershed friendly" by enrolling some of their land into conservation programs. (Prior to this project, the Little Cottonwood River had numerous areas where active floodplain had been farmed and was contributing significant amounts of nutrients and sediments to the river.)

CREP & CRP
Two very popular programs were the Conservation Reserve Enhancement Program (CREP) and the Conservation Reserve Program (CRP), both offered by the U.S. Department of Agriculture. As part of the project, Board staff promoted CREP and CRP through three steps.

• First, a letter was sent to all county landowners advertising the program.
• Second, this mailing was followed by another with a dollar per acre calculation, based on GIS photos and soil maps, that showed both which acres were eligible and the financial compensation the landowner could get for enrolling the property in the program. These mailings went out to all eligible landowners in the watershed.
• Third, Board staff called and visited the landowners to answer questions and help with the enrollment process.

Between CRP and CREP, more than 4,000 acres have been enrolled by an estimated 150 landowners within the 170 square-mile watershed. These land enrollments conserve about 16,000 tons of soil and prevent an estimated 4,500 pounds of phosphorus and 80,000 pounds of nitrates from entering the river each year. Enrolling these marginal areas into permanent and semi-permanent grass cover not only reduced sediment and nutrient loadings to the river, but also reduced the negative impacts of flooding.