The pool behind Lock & Dam #4 includes Lake Pepin, the largest lake that is part of the main river (not considering some of the lakes in the headwaters region that the river flows through). The dam does not, however, create Lake Pepin, the lake has been there since before the river was first mapped. What happens is geologically interesting. The river channel was carved 12,000 years ago when the glacial Lake Agassiz drained at the end of the ice age. The Chippewa River flows into the Mississippi just north of Alma, carrying with it a large load of sediment. Between 12,000 years ago and 9,500 years ago, that sediment accumulated to form a natural dam across the river channel. This dam caused Lake Pepin to form. Today, the lake is about 22 miles long, and averages 1 to 2 miles in width.

The dam itself has a rather small main structure, but a very long earth embankment. The dam consists 6 of the older style roller gates and 22 of the newer style Tainter gates. This is unlike Lock & Dam #3, just up river, which was opened about the same time. Lock & Dam #3 has only roller gates. The Lock & dam features a single lock 110 feet wide by 600 feet long, which is very typical of the upper river locks.