Waubay National Wildlife Refuge, located about 25–30 minutes off I-29 in southeastern South Dakota, is a haven for migratory birds and native prairie wildlife. Positioned roughly halfway between Sioux Falls, South Dakota (~2 hrs 10 min) and Fargo, North Dakota (~1 hr 50 min), it’s an ideal nature stop on a northern plains road trip or as a day trip from Sioux Falls.
The refuge spans over 4,600 acres of wetlands, grasslands, and woodlands, with scenic overlooks and peaceful trails—including a great loop hike on Headquarters Island, located in the northeastern section of Waubay Lake.
This location offers visitors great spots for a picnic, an easy hiking trail, and the chance to see a significant amount of wildlife up close. When I visited in the spring of 2025, I spotted whitetail deer, snakes, turtles, fish, and countless birds along the trail on Headquarters Island.
The Waubay Loop Trail
Wood Duck Way – Bur Oak Boulevard – Whitetail Way
Although the wildlife refuge spans over 4,000 acres, the main visitor area is located on Headquarter Island [Google Maps Link]. This area features a short loop trail that can be customized—either shortened or started and ended at different points along the route.
I recommend beginning and ending your walk at the visitor and education center, which is visible immediately after crossing the land bridge to the island. While parking is limited here, it is the largest lot available on the island. Since the loop trail intersects the road at two points, you can also choose to park near the observation tower or at the picnic area by the entrance to the boardwalk section of Bur Oak Boulevard.
The trail is flat and easy, measuring about 1 to 2 miles. It’s more of a pleasant walk than a strenuous hike.
Wood Duck Way
By starting at the education center, you will start the loop by taking Wood Duck Way.
The first 100 feet of the trail is a paved path that passes by a small pond and leads to a scenic viewpoint overlooking Waubay Lake, complete with a bench to take in the view. After this paved section, the trail transitions to a grassy path. This wildlife refuge sees so few visitors that the path is lined with lush green grass, a refreshing change from the usual dirt and stone trails I’m accustomed to.
Wood Duck Way is short walk that ends at the boat access point. While you can make a loop by turning right to the Tower and walking along the road, I recommend continuing straight to the Bur Oak Boulevard for a more extended experience. *Bur Oak Boulevard is much nicer than Wood Duck Way*
Bur Oak Boulevard
Bur Oak Boulevard is the longest trail on Headquarters Island. The first two-thirds of the trail follow the grassy path that loops around the eastern half of the island. Along the way, there are five benches—three located on the grass trail and two more in the boardwalk section, which makes up the final third of the trail.
This part of the hike is particularly special, offering constant views of the lake and scenic dead trees rising from the water, which serve as homes for various bird species. During my hike, I spotted numerous species of bird along this section of the trail.
Bur Oak Boulevard – Boardwalk Section
This is the most beautiful section of the island and offers the best wildlife viewing. During my hike, I spotted garden snakes, small turtles, countless birds, and numerous fish here.
While this trail is theoretically wheelchair accessible, during my visit, two smaller fallen dead trees were blocking the boardwalk, making it impossible for a wheelchair to pass through.
Whitetail Way
Once the boardwalk ends and the Whitetail Way trail begins is a couple picnic tables, and the only toilets on the island. They are vault toilets and were decently maintained.
Whitetail way is the least scenic section of the loop trail, and serves mostly as a natural alternative to walking along the road. However, I was pleasantly surprised to have spotted a smaller whitetail deer sharing the trail with me!
Exploring Headquarters Island
n addition to hiking the loop trail, this is a great spot for a picnic and possibly launching a non-motorized boat onto the water. Online sources mention that visitors can go up the observation tower, but when I visited in the spring of 2025, the tower was locked and access was restricted.
Planning a Trip: My Recommended Lodging
Staying near Waubay in Webster, SD
Tails Up Retreat – Great for big family trips and pet-friendly!
Staying near Lake Kampeska in Watertown, SD!
Budget-Friendly Accommodations in Watertown with Top Reviews
- My Place Hotel – Affordable, clean, and consistently well-rated.
- Holiday Inn Express & Suites – Offers complimentary breakfast and modern amenities.
Stay on Lake Kampeska in Watertown
- Cute Cabin on Lake Kampeska – A charming pet-friendly two-bedroom cabin with a queen bed, bunk bed, sofa bed, and an outdoor deck.
- The Retreat on Lake Kampeska – A luxury one-bedroom apartment with a terrace, swimming pool, and stunning lake views.
Happy Trekking!
-Aurora
