Raccoons are likely the primary nest predators, and red imported fire ants may threaten embryos and emerging hatchlings. American Alligators probably prey on smaller turtles, and carapacial pitting on some individuals appears to be from alligator tooth marks. In the lower Suwannee River, marine predators such as sharks may also pose a risk. Adult turtles are well-protected by their massive shells and powerful jaws, but hatchlings and juveniles are far more vulnerable. Leeches are common external parasites, and the blood parasite Haemogregarina macrochelysi—transmitted by leeches—has been detected in all individuals sampled.

This species does not truly hibernate or aestivate. It remains active year-round in the upper and middle Suwannee River, though activity likely decreases at low water temperatures. Captive individuals ceased feeding below about 18°C, and capture rates drop in winter. That said, active individuals have been observed snorkeling at night in the Santa Fe River during January and February at water temperatures of 16–20°C, and turtles have been captured in baited traps in December. Aerial basking is extremely rare—only a single observation of a juvenile basking in partial sunlight has been documented.

These turtles are opportunistic omnivores with a diet that shifts as they grow. Adults consume mostly fish—particularly sunfish—along with smaller amounts of crayfish, snails, plants, and macroalgae. They've been documented eating remarkably varied fare, including acorns, persimmon seeds, wild grapes, pawpaw fruits, green algae, musk turtle bones, and even a complete nine-banded armadillo skeleton. Juveniles rely more heavily on crayfish and small fish, which they lure into striking distance using their wormlike tongue appendage.

Adults are opportunistic scavengers and active nocturnal foragers, moving upstream from bank to bank in shallow water, periodically probing the substrate with their heads to smell out food. Interestingly, about 35% of persimmon seeds recovered from their feces germinated, suggesting these turtles may play a role as seed dispersers in their river ecosystem.

Much about the reproductive biology of this species remains poorly understood. Captive turtles courted from February through April, and the first wild mating observation occurred in December—the earliest mating ever recorded for any alligator snapping turtle. Male combat involving wrestling and head-biting has been observed in September, October, and December, suggesting the breeding season may be more prolonged than previously thought.

Nesting occurs from late March through mid-May, with females selecting partially open, sandy areas such as sandhill habitat, river bluffs, sand roads, and residential yards within 15–78 m of water. Known clutch sizes range from 16 to 47 eggs, with a mean of about 35—similar to the closely related Western Alligator Snapping Turtle. Eggs average about 38 mm in diameter and 31 g. Hatching likely occurs in August or September after roughly 100–110 days of incubation, with nest temperatures determining the sex of hatchlings: 25–27°C produces mostly males, while 29–30°C produces only females.

Sexual maturity is estimated at about 19 years for females and 22 years for males, and females likely produce only one clutch per year, with some occasionally skipping years.

What sets this species apart starts with its evolutionary isolation. Split from other alligator snapping turtles millions of years ago, the Suwannee population was recognized as a distinct species in 2014 based on genetic and morphological differences—including a uniquely wide, lunate-shaped notch at the back of the shell and a skull that is nearly as wide as it is long.

The wormlike lingual lure is perhaps the most famous feature of alligator snapping turtles. This pink appendage on the floor of the mouth is wiggled to attract curious fish into the gaping jaws—a sit-and-wait strategy that juveniles use masterfully. The lure's color can change over time and even between encounters, shifting among red, pink, gray, and white depending on blood flow and pigmentation.

The species' response to the Suwannee River's unusual geology is also remarkable. Population structure, body size, and sex ratios shift dramatically along the river as water chemistry transitions from acidic blackwater to mineral-rich, spring-fed conditions—providing a natural laboratory for understanding how environment shapes turtle populations.