The Johnson Creek watershed contains a mosaic of vegetation types, including agricultural lands, urban and suburban landscapes, upland forests, riparian woodlands, and wetlands. Because of extensive logging and clearing, remnants of pre-development vegetation are rare. About 57 percent of the watershed is currently vegetated, including grass, trees, blackberries and all other types of vegetation.
The forest that historically covered the Johnson Creek watershed ridges and lowlands was substantially cleared in the early 1900s for agriculture, timber production, and urban development. In the mid and late 20th century some areas such as the buttes and ridges in the south central and eastern part of the basin were left to regenerate into a second growth forest. Forest clearing of second growth has increased dramatically in recent years as housing development expanded from the lowlands onto the ridges and hillside slopes.
Over time, development and associated changes to the landscape have highly impacted the wetlands within the Johnson Creek Watershed. The remaining wetlands are extremely diverse. They range in size from the 19-acre Beggars Tick marsh in the Lents area, to many small emergent wetlands in the basin of less than a tenth of an acre.
Many wetlands in the basin have good connectivity with undeveloped open space, upland habitats, and the Johnson Creek riparian corridor. Several significant areas of wildlife breeding and nesting are found in wetlands within the basin with dense breeding populations of amphibians, including red-legged frogs.
Channelization and development have greatly reduced riparian vegetation throughout most of the Johnson Creek Watershed. In most of the watershed, riparian vegetation is narrow, minimal, or lacking. Thirty-four percent of the watershed has little or no riparian vegetation present, and an additional 32 percent has riparian vegetation less than 100 feet wide. The riparian corridors are also highly fragmented by frequent road crossings.
Generally, vegetation in riparian areas is dominated by blackberry or young native plants and lacks large mature trees. However, riparian area vegetation quality is improving. Local agencies and citizen groups have ramped up efforts to remove invasive and non-native plants and replant natives, creating more canopy closure.
Channelization of Johnson Creek has significantly impacted the quality of instream physical habitat. Because the historical floodplain is disconnected or minimally connected to the creek through much of its length, flood flows cannot spread out and soak into the floodplain. Rather, flood flows are directed and concentrated into the main channel, increasing stream bed scour and degrading instream habitat for fish and other aquatic organisms. Floodplain fill and disconnection also eliminated off channel habitat along the mainstem. Off-channel habitat is extremely rare, and is a major component of current restoration Projects like Kelley Creek.
Johnson Creek has extremely low volumes of instream wood, particularly large wood necessary for pool formation. In stream large wood is lacking because there are few large, mature trees along the stream banks. What large trees do fall into the creek are often removed to prevent potential damage and flooding.