A brown-water navy or riverine navy, in the broadest sense, is a naval force capable of military operations in inland waters (rivers, lakes and inland seas) and nearshores. The term originated in the United States Navy during the American Civil War, when it referred to Union forces patrolling the muddy Mississippi River, and has since been used to describe the small gunboats and patrol boats commonly used in rivers, along with the larger "mother ships" that supported them.

Brown-water navies are typically only used for patrolling and enforcing internal waters, in contrast to blue-water navies, which can independently conduct operations in the open oceans and project power far offshore. Green-water navies, which operate mainly in brackish estuaries, bays and shallow seas not too far off coasts (typically within the bounds of exclusive economic zones), fill the operational gap between brown-water and blue-water navies.

The River Thames was a regular thoroughfare for the Sovereign until the middle of the 19th century. Monarchs would be rowed up and down the river in a Royal barge, with transport and security organised by the King's Bargemaster. The barges were operated by the Royal Watermen, drawn from the ranks of the Company of Watermen and Lightermen. In 1798, Watermen and other groups of river tradesmen on the River Thames voluntarily formed associations of River Fencibles. These were officially drawn together in 1803 as the "Corps of River Fencibles of the City of London". Members of the Corps escorted the barge carrying the body of Lord Nelson along the Thames in small boats during his state funeral in 1806. The Corps of River Fencibles was eventually disbanded in 1813.

Both the Habsburg Empire and the Ottoman Empire maintained river flotillas on the Danube in 18th and 19th centuries, most notable for the use of šajka boats. Men who served in the Habsburg flotilla were known as Šajkaši.

After losing its blue-water fleet in the Battle of Copenhagen in 1807, the kingdom of Denmark-Norway quickly built a brown-water navy. The partial successes of the resulting Gunboat War were undone by land invasion.

During the Mexican–American War, Commodore Matthew C. Perry decided to invade the Mexican towns along the Gulf Coast near Tabasco. In October 1846 Perry was in command of USS Mississippi, USS Vixen, USRC McLane, USS Reefer, USS Bonito, USS Nonata and USRC Forward with a 253-man landing force. After capturing the port of Frontera on the Tabasco River, the ships under Perry's command crossed the bar at the mouth of the river and traveled 74 miles (119 km) up river to the town of Tabasco. After several days of bombardment of Tabasco, Perry's ships captured several Mexican ships on the river and brought them back to Frontera. Some were commissioned into U.S. Navy service and others were burned.

The city of Tampico was poorly defended and offered a base for operations for the conquest of the state of Tamaulipas. For these reasons Tampico became the next target for seizure by American naval forces. Commodore David Conner directed that it be attacked in late October 1846 and those plans were captured by General Antonio López de Santa Anna. Santa Anna directed that Tampico be almost abandoned and his forces be moved up river to Pánuco. This move was completed by 28 October. The bar at the mouth of the Pánuco River was only eight feet and hindered the movement of American ships up the river. The wife of the former American consul at Tampico sent word to Conner that the river was rising and that the town had been abandoned. Conner's forces crossed the bar on 14 November and began shelling the town. Almost immediately the remaining garrison at Tampico surrendered and Conner learned that the troops stationed there had retreated to Pánuco 25 miles upstream from Tampico. After Conner's ships moved to Pánuco and several days of naval bombardment, the Mexican forces at Pánuco surrendered. The American Army quickly occupied Tampico and used it for a staging point for a planned attack on Veracruz.

The U.S. Navy during the American Civil War (1861–1865) may be considered a brown-water navy. As a blueprint for the "strangulation" of the Confederate States of America, Winfield Scott's Anaconda Plan called for a two-pronged approach by first blocking the South's harbors and then pushing along the Mississippi River, effectively cutting the Confederate territory in two while also robbing the South of its main artery of transport. The U.S. Navy was assigned the blockade of the seaports, while a new force of gunboats and river ironclads, together with regular army units, would take, or at least lay siege to, the Confederate forts and cities along the Mississippi. In the early days of the war, U.S. Army built and crewed these boats, with the naval officers commanding them being the only direct connection to the U.S. Navy. By the autumn of 1862, the boats and their mission were transferred to the Department of the Navy. Because of the river's murky brown water, the ships that participated in these Mississippi campaigns were quickly referred to as the brown-water navy, as opposed to the regular U.S. Navy (which was henceforth referred to as the deep-water or blue-water navy).