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South Slough Reserve Habitats
South Slough Reserve Boardwalk
The Coos estuary and watershed contains a wide range of aquatic, terrestrial, and intertidal habitats, and a corresponding diversity of flora and fauna. The South Slough watershed presents an excellent microcosm of many habitats of the Coos estuary. However, there are three important differences between the Coos and South Slough watersheds: 1) the Coos estuary contains habitat types not found in South Slough; 2) the Coos estuary has sustained more intense development than South Slough; and 3) the Coos estuary generally experiences more tidal flushing and higher salinity than South Slough.
Biotic conditions and communities in the South Slough watershed, especially within the Reserve, are described in detail in, The Ecology of the South Slough Estuary: Site Profile of the South Slough National Estuarine Research Reserve.

Douglas Fir conifer
Upland regions of the Coos watershed are heavily forested with conifers, predominantly Sitka spruce (Picea sitchensis), Douglas fir (Pseudotsuga menziesii), western hemlock (Tsuga heterophylla), and Port Orford cedar (Chamaecyparis lawsoniana). The most prevalent broad-leaf evergreen tree is the Pacific wax myrtle (Myrica pacifica). Red alder (Alnus rubra) and willows (Salix spp.) are the predominant deciduous trees, especially in riparian areas.
The entire Coos watershed has been logged at some time in the past hundred years. Some areas contain recent clearcuts, and others have been planted exclusively with Douglas fir.  Understory plants include salmonberry (Rubus parviflorus), thimbleberry (Rubus spectabilis), blackberry (both the native Rubus ursinus, and non-natives Rubus procerus and Rubus lacianata), salal (Gaultheria shallon), evergreen huckleberry (Vaccineum ovatum), red huckleberry (Vaccineum parvifolium), and Pacific sword fern (Polystichum munitum). The forests contain a rich assemblage of additional shrubs, ferns, fungi, moss, insects, amphibians, reptiles, birds, and mammals. Deer, elk, raccoons, porcupines, opossum, owls, and bats are common; black bear, cougar, coyotes, and bobcats inhabit the more remote areas.
Upland areas of the South Slough watershed are typical of the Coos estuary and include 30 to 50 year old mixed conifer forests, recent clearcuts, and brushy slopes. The South Slough watershed also contains some small stands of trees over 80 years old, and occasional specimens estimated to be over 100 years old.

Freshwater Habitats
Skunk Cabbage in bloom
Riparian Zones
An abundance of streams drain the uplands of the South Slough watershed. The riparian areas are typically lined with red alder and occasional small willows). Streamside herbaceous communities are typically lush with Pacific sword fern, deer fern (Blechnum spicant) and lady fern (Atherium filix-femina), and often include Oxalis (Oxalis oregona).
Beaver live in and around streams they have dammed, while river otters establish regular pathways for passage into and out of streams. Riparian areas are believed to serve raccoons, deer, and other small mammals not only as sources of food and water, but also as corridors which facilitate movement to and from the estuary. South Slough tributaries provide habitat for amphibians such as the Pacific giant salamander (Dicamptodon tenebrosus) and the red-legged frog (Rana aurora), and many contain populations of resident and anadromous fish, such coho salmon (Onchorhynchus kisutch). Other tributaries in the watershed, for reasons now under study, appear virtually unpopulated by fish. Some streams, buried by brush and sediments from logging activities, no longer run above ground, and their biological attributes are unknown.

Fresh Water Ponds and Marshes
Freshwater wetlands and marshes in the South Slough watershed usually occur in direct association with streams, although some isolated wetlands exist in the uplands. Most of the larger freshwater wetlands occur in the extensive stream systems of the southern and eastern portions of the watershed. Freshwater marshes frequently form just up and downstream from leaky beaver dams, and in stream sediments which have accumulated immediately above the high tide line. Throughout the South Slough watershed, historic diking activities have artificially produced a number of freshwater marshes and wetlands.
Vegetation characteristic of freshwater wetlands includes sedges (Carex obnupta, Scirpus microcarpus), cattail (Typha latifolia), soft rush ( Juncus effusus), spike rush (Eleocharis spp.), burr reed (Sparganium emersum), skunk cabbage (Lysichitum americanum), and reed canary grass (Phalaris arundinace, an introduced species). Deeper marshes and ponds may contain duckweed (Lemna minor) and spatterdock

Hidden Creek Tide Channel
Saltmarshes support large populations of larval and adult invertebrates, which are consumed by the shorebirds and waterfowl that live in or visit the estuary. The Coos estuary contains less than 10% of its original saltmarsh habitat, due to fill, dredging, and other development-related disturbances. Significant portions of the saltmarshes remaining in the Coos estuary are found in South Slough. Marshes occur sporadically in the northern end of the Slough, and become larger and more frequent towards its southern reaches. All South Slough saltmarshes may experience less tidal influence than saltmarshes in the main Coos estuary waterbody, but the biological differences between the two areas remain to be studied.
South Slough contains high and low saltmarshes which have experienced varying degrees of disturbance and recovery. Plant communities of South Slough saltmarshes are typical of the region, and include tufted hairgrass (Deschampsia caespitosa), saltgrass (Distichlis spicata), pickleweed (Salicornia virginica), Baltic rush ( Juncus balticus), jaumea
( Jaumea carnosa), and Lyngby’s sedge (Carex lyngbyei). A few small marshes in the South Slough support the less common salt marsh bird’s beak (Cordylanthus maritimus) and sea lavender (Limonium californicum).

Emergent Islands
The South Slough estuary contains several low islands of a few hundred square yards, created by deposits of dredge  spoils during the past hundred years. These islands appear to provide habitat for invertebrates and feeding areas for some birds, but the biota of these islands, like the biota of the more tidally-flushed Coos estuary spoil islands, remain to be studied.

Mudflats and Channels
The sediments of the Coos estuary are primarily soft and unconsolidated. They create large mudflats which are exposed for extended periods during low tides. Most of the tidelands of the South Slough estuary are composed of mud or muddy sand. The mudflats are often partially covered by mats of Vaucheria (a green alga), and typically harbor cockles (Clinocardium nuttalli), gaper (Tresus capax), bentnose, and littleneck (Protothaca staminea) clams. Ghost shrimp (Callianassa californica), mud shrimp (Upogebia pugettensis), juvenile Dungeness crab (Cancer magister) also inhabit mudflats in the estuary. The mudflats are a rich feeding ground for a number of small shorebirds, and for great blue herons, egrets, and kingfishers.
Beds of eelgrass (both native Zostera marina, and the introduced Zostera japonica) cover an estimated 100 acres of the Coos estuary bottom. In late summer, up to 160 acres of eelgrass may be found in the Reserve, with additional beds of unknown size in the northern part of South Slough. These eelgrass beds, together with deeper tidal channels in the estuary, shelter a large number of fish and invertebrates. The blades of these plants create attachment area for algae, planktonic larvae, and snails. Eelgrass also provides cover for juvenile crab, juvenile ling cod, salmonids, starry flounder, English sole, and other fish and invertebrates. The plants’ height allows development of several vertical layers of structurally diverse and productive habitat.

Rocky Bottom
South Slough does not contain rocky or cobble-bottomed areas of significant size. The single known exception is at the northern end of the watershed, at the Coos estuary mouth, on intertidal land below a small cliff. This small rocky patch is occupied by a diverse community of hard-bottom and
boring invertebrates. These include barnacles, mussels, sea anemones, snails, and clams.

Sand Flats
Sandy bottom and sand flats are very uncommon in the South Slough. Within the Reserve itself, one sand flat area occurs off the northwest corner of Valino Island, and a second narrow strip runs along part of Long Island Point’s west shore.  A few coves north of the Reserve contain the only other sandy areas in the slough.