The park contains high-quality and relatively undisturbed examples of several natural communities, including ponderosa pine, woodlands, Douglas fir forests, Gambel oak thickets, and tall and mixed grass prairie.
Mesic oak thickets cover about half of Roxborough and are dominated by Gambel oak, mountain mahogany, buckbrush, skunkbrush, snowberry and yucca. Mixed grass prairie occupies relatively level areas where soils are deep and well-drained. Dominant grass species are western wheatgrass, green needlegrass, big and little bluestem, prairie sandreed, blue and side-oats grama and needle-and-thread grass. Douglas fir forms almost pure stands in steep, moist, north and east facing ravines in higher elevations, mostly near the western boundary. Ponderosa pine scrub woodlands occur on east-facing foothill slopes of the Dakota and Lyons Hogbacks in dry, shallow, rocky soils.
Tall grass prairie is dominated by big and little bluestem, yellow Indian grass, prairie sandreed, prairie dropseed and porcupine grass. Uncommon in Colorado, this natural community is thought to persist as a relict from cooler, moister times 10,000 years ago. Several small aspen stands also may be relict populations. The park was designated a National Natural Landmark in part for the atypical occurrence of tall grass prairie and low-elevation aspen groves.
A variety of riparian and wetland communities are present along Willow Creek, tributary drainages and on seeps and springs. Chokecherry, Rocky Mountain maple, Boulder raspberry and wax currant commonly grow along drainages. Several uncommon species on the park include Roxborough currant, wood lily, Joe-pye weed, yellow rockrose, pine drops pinesap and carrion-flower.