During the 2000 boating season, divers working for state and federal agencies discovered zebra mussels and zebra mussel reproduction in many parts of the St. Croix River downstream of Stillwater. Because of the widespread presence of zebra mussels on the river bottom, the Minnesota DNR designated part of the St. Croix River from the MNDOT Boomsite Recreational Area (river mile 25.4) downstream to the confluence with the Mississippi River, as infested waters containing zebra mussels. As a result of the establishment of the zebra mussel population, and efforts to prevent the spread upstream in the river and to other Minnesota waters, there are restrictions that boaters should be aware of when using and leaving the St. Croix River.
People who boat in the infested waters of the St. Croix River should take extra precautions to prevent moving zebra mussels to inland waters when they trailer their boats. Any boat leaving zebra mussel infested waters must drain all water before leaving the water access site. This means that water in live wells and the bilge must be pumped or allowed to drain by removing the drain plug, and any other water, such as in bait buckets, must be dumped out at the access site. These regulations are in addition to the statewide regulations that require removal of aquatic plants or attached zebra mussels from boats and other equipment. Boaters who leave their boats in the infested waters for more than a day during the summer should wash their boat with a hot water pressure washer, or dry their boat for at least five days. Day-use boaters pose less risk for spread, but should still inspect their boat, and consider washing or drying their boat. Both users must drain all water as described above, as well as removing all plants or animals.
There are no restrictions for boating south (downstream) from the Stillwater area on the St. Croix River. Neither state has restrictions prohibiting boat traffic between the Mississippi and St. Croix rivers. Boaters are encouraged to limit their travel in the heavily infested waters of the Mississippi River (Lake Pepin area and downstream) to avoid bringing more zebra mussels into the St. Croix.
Boaters who intend to head north (upstream) from the Stillwater area should be aware that the National Park Service (NPS) has restricted travel in the Federal zone at RM 28.5 (the High Bridge area). No boats will be allowed to travel north (upstream) past this point. Boaters who are traveling downstream can pass this area, but will not be permitted to travel back upstream.
Other than the statewide prohibition on placing a boat or trailer in the water with zebra mussels or aquatic plants attached, there are currently no other restrictions on launching boats at access sites north of the High Bridge area on the river (such as those at state parks or on the mainstem at Osceola) as long as the boater does not travel downstream beyond the NPS restricted area that ends near the High Bridge.