The Continental Army under George Washington had a habit of astounding the British.  While the British Army was composed of professional soldiers, the Americans were all men of other careers fighting for a cause.  Often, just when they had Washington and his army trapped with their backs to a body of water, the Americans would slip from their grasp.  Their were able to do this because of a regiment of fisherman from Marblehead, Massachusetts, who would ferry the army across bodies of water as soon as boats could be gathered.  Later, particularly in the War with Mexico, the Army depended upon the Navy for maritime movement. 
So, in 1861 the army in what was then called the west (Illinois, Indiana, and Missouri) faced a serious problem.  In a region where roads were few and poor, and rivers were the preferred mode of transportation, it was cut off from the navy by the confederacy.  Luckily, the war had idled most river traffic, and so an abundance of steamers were available for service as transports, but there were no warships to support them.
The navy was not interested in spending its limited funds on a western fleet, but they did send Commander John Rodgers to assist the army, and then take command of the fleet.  Rodgers was supplied with naval constructor Samuel Pook, who would design the vessels.  The ships Pook designed were like no others that had ever taken to water.  The shallow draft hull, 175 feet long and 50 feet wide, was like commercial vessels, but the machinery and paddle was placed inboard and covered with a stout casement of wood.  The forward slope of the casement was encased in iron, and three gun ports gave these ships an unusually strong forward battery. Four more gun ports were on each side, and two more protected the stern.  An armored pilot house sat atop the casement, and the wheel was housed over to protect it.  Because of their sloped sides, the vessels became known as Mr. Pook's Turtles, and were named after river cities; Cairo, Carondelet, Cincinnati, Louisville, Mound City, Pittsburgh, and St Louis.
The Contract to build the vessels was let by the War Department to James Eads, a local ship builder, primarily because he promised delivery by October 5, 1861, or the army could charge penalties against the contract.  The first launched was the St. Louis, on October 12, 1861, the first to enter service was the Carondelet, on January 15, 1862, becoming the first vessel in either US or CS fleets to carry iron armor.
Manning the ships presented a problem to the army.  500 artillerists were sent from the Washington DC defenses to man the guns, the Revenue Cutter Service sent 300 men from the coast, and there were men that were sailors from various army regiments.  Still lacking in men, civilian river men were hired to work aboard the ships as pilots, engineers, deckhands and coal heavers.  This last group men were employees of the army, rather then enlisted soldiers.  All the officers aboard the ships were provided by the navy, and many famous men got their first commands aboard these ships.
As they entered service, the ironclads joined a small group of converted  steamers turned gunboats.  A group of ships the army called its "Western Gunboat Flotilla."  The army also built a separate fleet of rams, and a fleet of fast steamers to transport regiments of its "Western Marine Brigade."  (which was never a part of the USMC.) Friction between the navy officers and the army officers in command of the other marine groups was common.  Rodgers was not popular with General Fremont, and so never got to command his fleet.  He was replaced with Captain A.H. Foote, who would lead the Flotilla into the history books, at the cost of his own life.
Eventually, the War Department transferred the Western Gunboat Flotilla to the Navy Department.  Sailors replaced the soldiers and civilians as crew and the ships took on the USS preface to their names they had not had as army vessels.  One result of the transfer was the renaming of the St. Louis.  She became the Baron De Kalb.  The navy already had a Sloop of War named USS St Louis, mandating the change. 

These ships were eclipsed by the later monitors and coastal warships, but for the early war period they carried the flag when no other ships were available and opened the Mississippi for the union.