In early historical times, the river had no defined banks, was filled with wet prairie grasses and forbs, and swelled or shrank in line with the seasons and with recent precipitation and runoff.

It stood adjacent to key commuter lines of the Chicago and North Western Railway and the Milwaukee Road (both now operated by Metra), and was valuable to developers as early as the late 19th century.

The wetlands were dredged and replaced with seven artificial lagoons as much as 16 ft (4.9 m) deep, in line with pastoral landscape appreciation patterns of the time.

The Forest Preserve District took some limited actions in the 1990s to alter some of the lagoons and try to restore a vestige of the original Skokie River wetland terrain.

In 2013, the Wilmette Golf Club, which is located in re-landscaped wetlands at the river's mouth, was scheduled to rebuild its grounds to reduce (but not eliminate) course flooding.

[2] As of 2013, the Forest Preserve District periodically restocks the Skokie River with fish matching some of the species present in early historical times, including bass, walleye, northern pike, channel catfish, bluegill, crappie, and bullheads.