Yes the USN was involved in several wars, and general occupation and police actions against Native American peoples. Most notably in the 2nd Seminole War in Florida from 1835 to 1842.

As a state with an enormous coastline, multiple rivers and waterways, and several large bays and harbor, it should be little shock that the Navy was ordered to assist the Army and local militia in the conflict. The Navy at the time maintained its West Indies Squadron at Key West, with other smaller bases in the Keys, Pensacola, and Tampa.

In addition to direct cooperation, the West Indies Squadron(and the Brazil and Home squadrons it was later absorbed by) had the mission of suppressing smuggling and piracy in the region. For the Seminole Wars in particular it was feared that Spanish flagged fishing vessels from Cuba were running arms and supplies to the Tribe. To combat this the West Indies Squadron had just 4 commissioned vessels, the frigate CONSTELLATION, the Sloops-of-War VANDALIA and ST. LOUIS, and the smaller schooner GRAMPUS.

In the early stages of the war the VANDALIA was dispatched to Tampa Bay to assist the land forces, both by providing armed small boats to conduct coastal patrols, but also by landing parties of sailors and marines to serve ashore.

This dual role dominated Naval contributions, what we would consider today to be Riverine or Green Water units were created and smaller vessels purchased and commissioned to allow for more patrols in coastal waterways. While shore parties augmented US Army and militia forces on land as well, a traditional and relatively normal thing for joint force operations at the time.

However it was not a smooth process, as the war dragged on and successive stratageies were tried and failed. However in 1840 after more fighting, including a raid on Indian Key that hosted a small naval depot, additional forces were committed. More small boats and canoes were ordered by the Navy, the Army purchased some more small schooners, and the Revenue Cutter Service(predecessor to the Coast Guard) offered several more small ships for use in shallow waters. And additional shore detachments were organized to assist the Army's plan to squeeze the Seminole forces in South Florida into what is now roughly Miami-Dade County.

Another minor note was the accomplishment of LT McGlaughlin, USN took over the Florida Expedition(the catch all for the assorted Riverine forces assembled) in 1839 and oversaw more aggressive operations into coastal and inland waterways. Specifically a force under his direct command of about 250 Sailors, Marines, and Soldiers went on a trek across the Everglades over the winter of 1840-41, a notable feat for the harsh environment, and size of the force.