In the report, the U.S. Army Corps of Engineers said the flood hit 119 counties along the lower Mississippi River states of Mississippi, Arkansas, Illinois, Kentucky, Louisiana, Missouri and Tennessee, causing $2.8 billion in damage.
The corps said they spent nearly $60 million while directly fighting the flood from March to August.
More than 21,000 homes and businesses and 1.2 million acres of agricultural land were affected, and more than 43,000 people felt some effects from the historic flood.
USGS said the Mississippi River and its Tributaries system operated as designed and was mostly successful in fighting the flood along most of the nation's most important inland waterway.
However, the spring floods exposed vulnerabilities in many parts of the system and the plans used to operate it. The report said there is room for improvement in nearly all areas.
"The magnitude of the event tested the system and its individual components like no flood before it," the report said.
Nearly all of the levee or floodwall systems experienced some damage. The floodways at Birds Point-New Madrid in Illinois, and the Morganza Floodway and Bonnet Carre Spillway in Louisiana were opened to relieve the stress on the system, marking the first time that three floodways had been operated during a single flood, the report said.
Levee-related problems that emerged included instability of levee slopes, seepage and sand boils, which are pools of water that bubble up near levees.
High water in and around Eagle Lake in Warren County, where levels were raised to offset pressure from the rising river, caused damage to piers and boat houses around the lake and affected boating and fishing.
The corps identified where repairs to levees and other parts of the system are needed and is using $802 million approved by Congress in 2011 to make critical and non-critical fixes "to prepare for the next high water event."
Most will be completed this year, but several "critical repair" projects are expected to extend into 2015 and 2016.
The Mississippi River rose to all-time record highs after excessive rainfall combined with snow melt across the Central U.S. through the Ohio River Valley in the spring of 2011. Nearly 5,000 Mississippi residents were displaced and one person drowned in the Vicksburg area.