The rivers, tributaries, associated hardwood and cypress swamps, and marshes provide food, shelter and breeding sites for many native species, as well as several designated as endangered, threatened, rare, or of special concern.

The wide diversity of plant communities found in the Wekiwa provides year-round food and protective cover for equally diverse and abundant animal populations. Each plant community provides food in the form of seeds, nuts, berries and foliage during different seasons.

The Wekiva River preserve has a variety of plant communities that maintain a high species diversity and biological richness. They range from the high, dry sandhills and sandpine scrub to river swamp. The unique natural feature of the preserve is the system of blackwater streams and their associated wetlands which provide superb habitat for a variety of rare and endangered animals. The Florida black bear, river otter, American alligator, wood stork, sandhill crane, indigo snake and a variety of more common native species may be observed while canoeing through or hiking in the preserve.

The Wekiva and Middle St. Johns Rivers consist of extensive areas of floodplain wetlands, including floodplain marsh, floodplain swamp, blackwater streams, and spring-run streams. Mixed hardwood trees such as tupelo, red maple, water ash, bald cypress, hickory characterize floodplain vegetation, laurel oak, and sweet gum. Other common plant species include wax myrtle, buttonbush, and swamp dogwood. Eelgrass is the dominant submerged vegetation.

An extensive floodplain of hardwood forest, approximately three miles wide in some areas, provides natural habitat for a diverse array of wildlife. Threatened plant species such as the needle palm, butterfly and water orchids, and Florida shield fern, are also found along the Wekiva