Brown-water navy is a term that originated in the United States Navy, referring to the small gunboats and patrol boats used in rivers. A broader meaning is any naval force that has the capacity to carry out military operations in river or littoral environments.
The term is used in contrast to the terms "green-water navy" and "blue-water navy". At one time, it was common to refer to all non blue-water navies as "brown-water navy". Today blue-water navies are generally defined as being capable of sustained oversea deployment, preferably with aircraft carriers, while green-water navies are defined as those with frigates or better, operating in coastal and regional area.
The brown-water navy is generally defined as one with patrol boats operating in rivers, lakes, and littoral regions. Being a brown-water navy does not imply that it lacks offensive capability, as many small littoral-combat ships today are armed with powerful anti-ship missiles.
The term brown-water navy originated in the American Civil War (1861-1865). 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 on, the Confederate forts and cities along the Mississippi. In the early days of the war, these boats were built and crewed by the U.S. Army, 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).
On 18 December 1965, for the first time since the US Civil War, the US Navy formalized the new Brown Water Navy in Vietnam. Its primary mission would be to interdict enemy re-supply, and any unauthorized contraband which might contribute to the enemy's war effort. In the beginning, the brown-water navy patrolled the inland waterways, primarily with South Vietnamese river craft (RAG-River Assault Groups) which had been mostly inherited from the French during their war; which in turn, had been received from the US, as military aid, during the French fight against the Viet Minh (Vietnamese Communists). As the new fiberglass PBR (Patrol Boat, River), using water jet propulsion, became available, it became the main interdiction vessel for the inland waterways. For close coastal waters during the war, more seaworthy South Vietnamese Navy water craft were used, until replaced by newer US Navy and US Coast Guard patrol vessels, such as the Coast Guard 82 footers, and US Navy Swift Boats (PCF-Patrol Craft Fast, aluminum 50 footers). By the late 1960s, the Swift Boat would commence operations alongside the PBR's in the inland waters, as well as maintaining operations along the coast line. The brown-water navy was a joint venture between the Navy and the Army, modeled after the earlier French Riverine and coastal patrols in the First Indochina War (1945-1954). In the beginning this force consisted of mostly modified surplus US WWII Landing craft (boats), such as the LCMs, LCVPs, LCIs, etc. The only entirely new riverine boat from the French Indochina War had been the French designed STCN (an all steel "V" hulled boat, approximately 40 feet in length, whose design had been influenced by the US LCVP). This particular craft influenced the design of the US Navy's only original riverine boat built for the Vietnam War; the 50 foot all steel hull, aluminum super-structured ASPB (Assault Support Patrol Boat, better known as the "Alpha Boat"). The "Alpha" boat was built by the Gunderson Company, in Oregon, USA, and was of reinforced construction, in order to survive exploding mines. As a consequence, the ASPB earned a reputation as the "mine-sweeper" of the riverine forces. Other riverine craft included, along with the aforementioned PBRs, PCFs, and ASPBs, were the PACVs (Patrol Air Cushion Vehicles), Coast Guard 82 footers, and the Monitors (modified LCMs). Together these craft formed a Mobile Riverine Force, that utilized various supporting facilities, such as the Yard Repair Berthing and Messings, advance bases, LSTs, helicopter and seawolf units. 
The brown-water navy was largely successful in its tactics to combat infiltration and weapons smuggling during its existence between 1965 and 1970. The units were formalized in January 1967 with the 2nd Brigade, 9th Infantry Division arriving under the command of Major General William Fulton. Later that same year, in combination with US Navy Task Force 117 they formed the Mobile Riverine Force. In 1970, for the first time since the US Civil War, the US Navy stood down the last of its brown-water navy units; as they were turned over to the South Vietnamese Government, during the US Navy's phase of Vietnamization.
U.S. Marines began patrolling the inland waters of Iraq soon after the beginning of the Iraq War, using a variety of patrol boats. In 2004 the Marines received a new type of fast boat, the small unit riverine craft (SURC), to patrol the waters of the Euphrates River and deny water passage to the insurgents. Beginning in 2006, the Navy established the Riverine Squadrons to assume this task from the Marines. A Riverine Squadron was deployed to Iraq in March 2007 and has been patrolling the waters of the river around the Haditha Dam.