The 40-acre woodland at Homestead is classified as a mesic bur oak forest, a rare community type in Nebraska. Upon acquisition of the Freeman homestead by the National Park Service, much of the wooded area along Cub Creek had been heavily grazed, and most of the older trees had been harvested. However, approximately 20 acres of woodland remained undisturbed. In 1939, 10,000 oak and hackberry seedlings were planted in the most disturbed area of the woodland, and by the 1960’s, much of the forest had recovered.

Dominating the riparian woodland area are several species of oak, silver maple, hackberry, and eastern cottonwood. The understory contains species such as wood nettle, false nettle, wingstem, sedges, and Virginia wild rye. Shrubs and young trees are present mostly along woodland margins and include coralberry, oaks, elms, and black walnut.

Another notable feature is the historic Osage-orange hedgerow, which was planted along the south boundary of the property by Daniel Freeman. Osage-orange (Maclura pomifera) is native to parts of Texas and Oklahoma but was commonly planted along hedgerows in Nebraska and other Midwestern states.