TPC Deere Run has achieved designation as a "Certified Audubon Cooperative Sanctuary" by the Audubon Cooperative Sanctuary System (ACSS), the educational division of Audubon International, endorsed by the United States Golf Association. In 2004, TPC Deere Run joined the Audubon Cooperative Sanctuary System, which provides information and guidance to golf courses to help them preserve and enhance wildlife habitat and protect natural resources.

To reach certification, a course must demonstrate that they are maintaining a high degree of environmental quality in a number of areas. These categories include: Environmental Planning, Wildlife & Habitat Management, Outreach and Education, Integrated Pest Management, Water Conservation, and Water Quality Management. Golf courses from the United States, Canada, and Europe have also achieved certification in the program.

General Manager Kirk Deneke stated, "Our entire staff here at the TPC Deere Run is very proud to have completed the certification process and to have been recognized as a Certified Cooperative Audubon Sanctuary. We are looking forward to continually improving the quality of our wildlife programs and to setting an example by proactively managing the way we work with our natural environment each day. Our superintendent and his team have worked diligently on this process and I commend them for their dedication to its completion and for their continuing commitment to the future impact of this outstanding program.