Passing through the cities of Gresham, Portland, and Milwaukie, the creek flows generally west from the foothills of the Cascade Range through sediments deposited by glacial floods on a substrate of basalt.

In the 19th century, non-Native American settlers cleared much of the land for farming, and the stream is named for one of these newcomers, William Johnson, who in 1846 built a water-powered sawmill along the creek.

In the 1930s the Works Progress Administration of the federal government lined the lower 15 miles (24 km) of Johnson Creek with rock to control the floods.

Shortly thereafter, Johnson Creek passes the USGS gauge station at Sycamore, 10.2 miles (16.4 km) from the mouth, and flows under Cedar Crossing Bridge.

Johnson Creek passes under Interstate 205, and shortly thereafter begins to flow more swiftly again at Southeast 82nd Avenue, about 8 miles (13 km) from the mouth.

After passing under Oregon Route 99E (Southeast McLoughlin Boulevard) in Portland's Sellwood neighborhood, the creek turns sharply south about 1.5 miles (2.4 km) from the mouth.

The lava, exposed mainly in the uplands, has been folded and faulted to form a series of sub-basins, including the Johnson Creek watershed.

[11] Formed by the ancestral Columbia and Willamette Rivers, the terraces north of Johnson Creek are generally underlain by permeable sand and gravel.

[13] About 40 percent of the tributaries that originally flowed over the surface of the watershed were piped or relocated during urban development, especially on the north side of the main stem.

[2] Fill at Foster Road and Southeast 111th Avenue usually prevents stormwater runoff from a 9-square-mile (23 km2) area of the watershed in the Lents and Powellhurst-Gilbert neighborhoods from flowing directly into the creek.

Normal drainage patterns have also been altered further downstream in the Sellwood, Eastmoreland, Westmoreland, and Woodstock neighborhoods, where runoff flows into the Portland sewer system instead of into the creek.

[15] 19th-century maps also show numerous springs and small streams flowing into a wetland that covered an area of today's southeast Portland between Powell Boulevard (U.S. Route 26) and Johnson Creek, a distance of 2.25 miles (3.62 km).

Its projects involve such things as controlling invasive species, planting native riparian vegetation, improving fish passage, and creating off-channel flood storage.

[12] In 2015, Portland's Bureau of Environmental Services (BES) began issuing annual "report cards" for watersheds or fractions thereof that lie within the city.

Hydrology grades depend on the amount of pavement and other impervious surfaces in the watershed and to what degree its streams flow freely, not dammed or diverted.

Water-quality grades are based on measurements of dissolved oxygen, E-coli bacteria, temperature, suspended solids, and substances such as mercury and phosphorus.

The area was the home of the Clackamas Indians, a subgroup of the Chinookan speakers who lived in the Columbia River Valley from Celilo Falls to the Pacific Ocean.

Epidemics of smallpox, malaria, and measles reduced this population to 88 by 1851, and in 1855 the tribe signed a treaty surrendering its lands, including Johnson Creek.

[24] By the middle of the 19th century, the European American newcomers had begun to remove vegetation, build sawmills, fell trees, fill wetlands, and farm in the fertile soil along Johnson Creek.

[25] In early 1848 Lot Whitcomb, who would later found Milwaukie, filed a donation land claim and built a sawmill near the confluence of Johnson Creek and the Willamette River.

[28] By removing the original vegetation, rural and urban development of the Johnson Creek watershed induced more rapid storm runoff and destructive floods.

[32] The USGS peak streamflow data collected by the stream gauge at that station show that the creek reached or exceeded 1,200 cubic feet (34 m3) per second 37 times between 1941 and 2006; that is 37 floods in 65 years.

[37] In 1990, the City of Portland formed the Johnson Creek Corridor Committee from multiple agencies and citizen groups with varied interests related to the watershed.

Studies suggest that most pollutants of Johnson Creek do not come from point sources but are washed off urban and rural land surfaces during storms.

[13] Studies conducted by DEQ, USGS, the City of Gresham, and other public agencies have identified DDT (dichloro-diphenyl-trichloroethane), dieldrin, polychlorinated biphenyls (PCB), chlordane, and polycyclic aromatic hydrocarbons (PAH) as carcinogenic pollutants of Johnson Creek.

[48] Common species in the 21st century include crow, robin, starling, song sparrow, Bewick's wren, house finch, cedar waxwing, violet-green swallow, belted kingfisher, great blue heron, mallard, wood duck, bushtit, black-capped chickadee, raccoon, opossum, nutria, and moles.

[49] Such animals known to live in the Johnson Creek watershed include long-toed, northwestern, and Columbia salamanders, red-legged frogs, painted turtles, great horned owls, toads, hawks, and coyotes.

It was covered until the mid-19th century with Oregon ash, red alder, and western redcedar forests and scattered black cottonwood groves in riparian areas.

[10] In 2000, about half of the rural agricultural total in the watershed consisted of cultivated crops or pasture, while tree farms and ornamental nurseries made up about 30 percent.

City parks adjacent to Johnson Creek have areas devoted to marsh with shrubs, cattails, and smartweed, forested wetland, riparian woodland, open meadow, and orchard trees.