The watershed vegetation has been drastically modified by European settlers through sheep and cattle grazing, logging and farming in the valley floors.

The creek once flowed through extensive wetlands at its mouth, but these were mainly drained to create farmland, apart from Rodman Slough on the west side.

[1] It flows south for 8.5 miles (13.7 km) to join Scotts Creek to form Rodman Slough.

[2] The Middle Creek watershed is underlain by the Franciscan Complex, a chaotic assembly of sediments and ocean floor scraped up by the advancing North American Plate.

[8] During periods of heavy runoff, the two creeks raise the level of the slough and the water moves at significant speed.

[11] At the start of the historical period the watershed was mostly occupied by Eastern Pomo, but they were in contact with Northern Pomo, with whom they intermarried[7] The arrival of Europeans devastated the native population, who died of new diseases and were forced to relocate and to work for the Europeans on pain of severe punishment or death.

Higher lumber prices after World War II (1939–1945) cost-justified construction of roads into almost all the timbered area of the watershed.

Robinson Lake was a mosaic of shallow wetlands, meandering channels, riparian forest and open water.

[9] As part of creation of the Edmonds Reclamation District in 1926 Clover and Middle Creeks were rerouted to their present locations, flowing south into Rodman Slough.

[15] The heavy earth-moving equipment used to "reclaim" about 2,000 acres (810 ha) of wetland was one of the causes of a surge in sedimentation in Clear Lake after 1927.

[18] The Middle Creek Restoration Project plans to remove 3 miles (4.8 km) of substandard levees.

The Army Corps would cover 65% of the costs, but the water district had to compensate over 60 private property owners, raise a section of California State Route 20, reinforce seven PG&E power line pylons and replace a bridge on the Nice-Lucerne Cutoff.