Historically, the Missouri River floodplain in this area contained wetlands, oxbow lakes and meandering streams draining out of the nearby bluffs, as well as a mix of floodplain forests, grasslands, sand dunes and shrub thickets. Periodic floods from the river provided biological and nutritive interchange between the river and the floodplain and tributaries. The wetlands and terrestrial areas were integral components of the floodplain system, providing seasonal habitat for river fish, and enabling diverse species both resident and migrant to find habitat. Senescing wetlands were replaced by new oxbow wetlands as the river meandered.

The historic ecological functions had been diminished or lost because of river channelization, upstream reservoir operations and agricultural and other development in the floodplain. This project was enacted to restore not only Nathan's Lake, but also the adjacent Deer Creek and Mud Lake wetland. By managing water levels and deepening Nathan's Lake and Deer Creek - fish, small organisms and nutrients would be enabled to move freely between the river and wetlands. Natural vegetation was also restored, further enhancing the remnants of these historic wetlands.

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