The bridge is the eastern terminus of Iowa Highway 2, and the western terminus of Illinois Route 9. Iowa 2 runs westwards towards Farmington, Iowa (23 miles/37 km), while Illinois 9 continues eastwards towards Canton, Illinois (~80 mi/129 km) and Peoria (~100 miles/162 km). On July 26, 1927, operations were transferred from the original single track bridge to the current bridge. The first opening for river traffic occurred at 11:58 a.m. on July 26, 1927, for the scow C. W. Howell traveling downriver with no barges attached.
The bridge is privately owned by BNSF Railway. Amtrak's Southwest Chief crosses the bridge with one eastbound train in the afternoon and one westbound train in the evening. The station is two miles (3 km) to the west of the bridge. 75 to 90 trains cross the bridge in a typical day.
Per Coast Guard regulations and the BNSF Fort Madison River Bridge operations manual, river traffic has the right-of-way over train and vehicle traffic on the bridge. The length of time for an opening varies due to weather, river current, size and number of boats, and occasional mechanical problems. A typical opening for a tow with 15 barges will take 15 to 20 minutes. The bridge logs over 2000 opening per year.
Bridge toll is charged only to those crossing from from Iowa into Illinois, and depends on the type of vehicle and number of axles the vehicle has. As of July 2008 the rates are: motorcycles 50 cents, automobiles and pick-up trucks $1.00, trucks larger than a pick-up truck are $2.00 per axle, not including the first axle, buses and RVs are $4.00, add $1.00 additional to any fee if towing a trailer, bicycles are free and pedestrians are prohibited from walking on the road or rail decks. All fees are cash only, no passes, checks or credit/debit cards are accepted. Also, any legal vehicles over wide and high are prohibited from crossing the bridge.