[clarification needed] This slow speed, combined with the abundant leaf-drop from nearby trees, especially Bald Cypress, leads to a very dark-brown river due to dissolved tannins.

[5] The land over the underground section of the river, referred to as a natural bridge, was used for the main route of the Spanish mission trail and the Bellamy Road to avoid a water crossing of the Santa Fe River.

[6] Springs like Gilchrist Blue, Ginnie, Hornsby, Lily, Poe, and Rum Island springs are located at the banks of the river, mostly downstream of the river's reappearance above ground level.

[8] The area is sparsely populated compared to the rest of Florida, there have been sightings of animals like the black bear, bobcat, the rare Florida panther and due to the near-constant water temperatures along many portions of the river, manatees.

[9] As with many rivers in Florida, plant and animal fossil remnants are plentiful along the Santa Fe.