The east branch begins with numerous seeps and rivulets feeding into Hensingersville Dam in Lower Macungie Township.

[4][5][6] Three intermittent runs feed Swabia Creek in the upper alluvial plain between Alburtis and Macungie.

The Gehman Road run passes the Allen Organ headquarters and Mack Trucks assembly plant.

After Maple Grove, the west branch flows along a depression created by a fault where the ancient crystalline gneiss of Lock Ridge erupts through the Leithsville formation.

The same progression in surface geology (gneiss, quartzite, dolomite) occurs for the east branch and Mountain Creek.

[17][18][19] Soils in the alluvial plain from Alburtis to Little Lehigh Creek are silt loams, such as Lindside and Melvin series.

The wetlands are listed as temporarily flooded palustrine systems containing broad-leaved deciduous forest, shrubland, or reeds.

The Macungie watershed, through which Mountain Creek flows, contains Northern Appalachian circumneutral seeps natural community which can support diverse threatened or endangered plants.

South Mountain is generally dominated by tulip tree, sweet birch, red oak, and silky dogwood.

[21] Common undergrowth includes jewelweed, bulrush, poison ivy, Virginia creeper, and fox grape.

Native plants growing in the alluvial plain include vervain, jewelweed, boneset, lobelia (including cardinal flower), sedges, aster, Joe-Pye weed, dwarf bluestar, black eyed susan, golden ragwort, goldenrod, red swamp mallow, redtwig dogwood and river birch, and dogwood.

[23][24][25] Permanent avian residents of Reimert Memorial Bird Haven, near the Mountain Creek headwater, include red-bellied, downy, and hairy woodpeckers, and white-breasted nuthatches, black-capped chickadees, tufted titmice (commonly called "warblers"), northern cardinals, blue jays, and non-native house finches.

[21][26] In August 2005, the Pennsylvania Department of Environmental Protection performed a geomorphic assessment and found that agricultural sedimentation and urban runoff were impairing water quality, degrading aquatic habitat, destabilizing the channel and banks, and causing other negative impacts.

The assessment recommended implementing specific best management practices, including establishing native vegetation and use of natural stream channel design, to improve habitat quality and floodplain function.

This designation may result in development of a conservation greenway that includes large portions of the Swabia Creek watershed.

As the name of the creek suggests, many early European settlers in the vicinity were from Swabia (German: Schwaben).