The park's habitat diversity, ranging from coastal rainforest to riparian and estuarine marsh, shrub, and swamp wetlands, is responsible for its high diversity of plant and fungi species.
More than 250 species of vascular plants and 74 of mosses and liverworts have been documented during recent surveys, and most are represented in the park herbarium. The various park units contain a diversity of habitats that provide niches for a wide variety of plant species.
The Sitka spruce vegetation zone forms a narrow band along the Pacific Northwest coast from southeastern Alaska to northern California. The moist, temperate maritime climate and deep, humus-rich soils create ideal growing conditions for conifer trees, resulting in climax spruce-hemlock forests of lush biodiversity and trees of massive size. Sitka spruce (Picea sitchensis) and western hemlock (Tsuga heterophylla) are the park's dominant conifer species. Western red cedar (Thuja plicata), Douglas fir (Pseudotsuga menziesii), red alder (Alnus rubra), cascara (Rhamnus frangula), red elderberry (Sambucus racemosa) and several willows (Salix species) are also common. Salal (Gaultheria shallon), huckleberries (Vaccinium species), and many ferns, mosses, liverworts, and lichens share the forest understory. In November of 1805, explorer William Clark described the coastal forest at Cape Disappointment: "Spruc Pine grow here to an emense Size & hight maney of them 7 & 8 feet through and upwards of 200 feet high ... I observed in maney places pine of 3 or 4 feet through growing on the bodies of large trees which had fallen down, and covered with moss." Most of these giant trees were cut for timber between 1850 and 1950. Today the majority of the park's forestlands are 30-50 year old mixed conifer stands in various stages of regeneration. The oldest spruce trees, at more than 100 years of age, can be found on Cape Disappointment and surrounding the Fort Clatsop replica. The Cape Disappointment forest has a multilayered canopy with a diverse understory, open clearings, dead snags and decaying logs, the hallmarks of a healthy old growth ecosystem. Sitka spruce to 36 feet in circumference provide habitat for nesting marbled murrelets, northern flying squirrels and many other arboreal dwellers.
Along with its expanse of forestlands, the park also preserves valuable estuarine resources within the nationally significant Columbia River estuary, including shoreline habitat on the lower Columbia and tidally-influenced Lewis and Clark Rivers with many low-gradient brackish sloughs and marshes. A number of streams, springs and freshwater ponds are also found in the park. In February of 1806, Meriwether Lewis remarked on the plants of these coastal wetlands: "The grasses of this neighbourhood are generally coarse harsh and sedge-like, growing in large tufts ... the salt marshes also produce a coarse grass, Bull rushes and the Cattail flagg." During the 19th and early 20th centuries most of the river shores were diked and tidegated, converting extensive floodplains to agricultural and industrial uses. In 1961 the National Park Service restored several acres of shoreline pasture at Fort Clatsop to a functional high tidal marsh that now supports a diversity of estuarine plants including Lyngby's sedge (Carex lyngbyei), common cattail (Typha latifolia) and narrowleaf cattail (Typha angustifolia), a species uncommon to the west coast. Two rare estuarine plants, flowering quillwort (Lilaea scilloides) and smallflower water pimpernel (Samolus valerandi ssp parviflorus), grow on the tidal mudflats and slough banks of the Lewis and Clark River. The Fort Clatsop unit also contains several acres of willow scrub-shrub wetlands, a habitat type that has largely disappeared from the Columbia estuary over the last century. A resident Roosevelt elk herd frequently browses this willow swamp in winter. Species and natural hybrids of two lovely native jewelweeds, the spotted touch-me-not (Impatiens capensis) and spurless touch-me-not (I. ecalcarata), are also found in these willow wetlands, the westernmost extent of a linear hybridization zone that extends for 30 miles along the lower Columbia River. At Cape Disappointment, coyote bush (Baccharis pilularis) is at the northern limit of its range and is the only recorded occurence of this species in Washington state. Two other rare plants recently noted at Cape Disappointment are floating marsh pennywort (Hydrocotyle ranunculoides) and seacliff bluegrass (Poa unilateralis).
Many areas of the park have a long history of agricultural and residential land use, and, consequently, a third of its vascular plant species are nonnative. Ongoing invasive species control projects target a number of these exotics, including Scotch broom, purple loosestrife, English ivy, holly and yellow iris.
Collecting plants in the park is prohibited without a National Park Service permit.