Here the tributaries of the Big Muddy are tiny, intermittent streams, meandering though these narrow valleys at the headwaters. The steep Illinoian hills are suddenly truncated where they meet the flat bottom of the Wisconsinan Era lake bed. Here the outline of the Wisconsinan Era lake bed is evident in what were the northern reaches of the ancient lake, where the lake bed was only a few hundred feet wide. The upper reaches of the Big Muddy are near Dix, Illinois. When the Big Muddy flooded, the water covered the flat bottom of the ancient lake bed for miles either direction from the meandering channel. Prior to the construction of Rend Lake, much of the ancient lake bed was swamp: a forested area that was covered by water through most of the winter, and during wet summers. The Pine Hills are loess hills standing several hundred feet above the floodplain.

At the edge of the floodplain, dunes, called 'loess hills', formed. Winter winds created dust storms that covered Southern Illinois with ' loess', fine grained, wind born deposits. During the winter the flow of meltwater was cut off, and the floodplain was a wide stretch of exposed mud. During the melting of the Wisconsinan glacier, the Mississippi River flood plain was filled with rushing meltwater in summer. The Pine Hills are bluffs overlooking the Big Muddy as it flows through La Rue swamp. The Big Muddy joins the Mississippi River in Jackson County near the La Rue-Pine Hills Ecological Area and less than 1 mile (1.6 km) south of Grand Tower Island. This is why the Big Muddy tends to be so muddy. This channel meandered in the flat bottom of the Wisconsinan-era lake. A new channel formed within the old lake bed. After the melting of the Wisconsinan glacier, the level of the Mississippi dropped, allowing the lake to drain. The ancient lake silted in, forming a flat bottom. Water backed up into the Big Muddy Basin, forming a lake much like the artificial Rend Lake but covering a larger area. However, during the melting of that glacier, the level of the Mississippi River was much higher.

The Big Muddy was not covered by the Wisconsin Glacier, about 70,000 to 10,000 years before present.

The Big Muddy basin formed after the retreat of that glacier. The watershed of the Big Muddy was covered by the Illinoian Glacier about 300,000 to 132,000 years before present. Pollution sources include agricultural practices, mining and municipalities. In 1995, water quality was assessed as 'fair' to 'good'. The Big Muddy drains a 2,344-square-mile (6,070 km 2) watershed.

Mud river launch ramp