The alluvial aquifers beneath the floodplains of the Mississippi and Missouri rivers are some of Missouri's most valued water resources. These aquifers are capable of yielding from 500 to more than 2,000 gallons of water per minute to properly designed and developed wells, and are widely used for municipal water supply and agricultural irrigation.

The alluvial materials of the valley are composed of clay, silt, fine to coarse sand and fine to medium gravel. The size of the alluvial materials typically increases with depth; finer-grained materials directly underlie the land surface and coarser sands and gravels are found at greater depth. This clay or silt cap overlying the more permeable sands and gravels, where present, will retard infiltration of surface water. Since these sediments were deposited by a meandering stream over long periods of time, there is no definite sequence of deposition at any particular site. The alluvium ranges in thickness from a featheredge at the edge of the valley to as much as 170 feet. The alluvium generally is thickest in the center part of the valley near the river, but there are instances where the thickest materials are near a valley wall. The volume of water stored in the Mississippi and Missouri River alluvial aquifer varies somewhat, but is estimated to be about 4.88 trillion gallons.

The Mississippi and Missouri river alluvium receives recharge from four sources: infiltration from the river, from bedrock adjacent to and underlying the alluvium, from precipitation falling upon the floodplain, and from downward leakage of water from streams flowing across the alluvium. Water from the river generally recharges the alluvium when one of the following conditions exists. When the river is at a high stage, there is recharge of the alluvium from the river. Recharge also occurs where high-yield wells are constructed close enough to the river so that when they are pumped they induce direct recharge from the river to the well. The groundwater surface of bedrock aquifer units adjacent to the Missouri River normally is above the groundwater surface of the alluvial aquifer. Thus, there is groundwater movement from the bedrock into the alluvium. The volume of water supplied to the aquifer by precipitation, and the volume of recharge that occurs from other streams as they cross the river alluvium, depends greatly on the characteristics of the shallow alluvial materials. In areas where the surficial materials are sandy and permeable, the amount of recharge water is significant. Where there is a clay or silt cap overlying the more permeable deposits, the recharge is less.

The Mississippi River forms most of the eastern border of Missouri. Its total length in Missouri is 485 miles. This includes approximately 123 miles where it borders the Missouri Bootheel. A comparison of geologic maps of Illinois and Missouri quickly shows that the Mississippi River tends to follow the bluff line on the Missouri side of the river. With the exception of the Southeastern Lowlands, there are only a few locations in eastern Missouri where there is a significant amount of Mississippi River alluvium. These occur in eastern Clark and extreme northeastern Lewis counties, eastern Marion County and extreme southeastern Lewis County, eastern Pike, Lincoln and St. Charles counties, a small area in eastern St. Louis County, a small area in eastern Ste. Genevieve County, and an area in northern Perry County. The total surface area of Missouri that is underlain by Mississippi River alluvium, excluding the Bootheel, is approximately 440 square miles. With such localized and small geographic distribution, the alluvium of the Mississippi River is not considered a major water source in Missouri. However, locally it is a very significant resource.

The Missouri River forms the western border of Missouri between Iowa and Kansas City, and bisects the state between Kansas City and St. Louis where it enters the Mississippi River, a total distance of about 533 miles. Like the Mississippi River, the Missouri River has carved a valley that contains up to about 150 feet of highly-permeable alluvial sediments. The alluvium underlies the Missouri River floodplain, which in Missouri ranges in width from zero, where the river hugs the bluff line in several places, to a maximum of about 12 miles. In general, the valley is widest upstream from Glasgow in Howard County. Between Glasgow and St. Louis, the valley generally is two to three miles wide.

The Missouri River alluvium is a very important and widely used water source in Missouri. Twenty-five counties in Missouri border the Missouri River, and nearly all of them make use of water available from the alluvium. Wells drilled into the alluvium supply much of the water for numerous rural water districts, towns and cities including Kansas City, Independence, Columbia and St. Charles. In addition, hundreds of high-yield irrigation wells are used throughout the reach of the Missouri River to enhance agricultural production.