Little is documented about predation on mata matas. Giant river otters have been observed bringing adults ashore and occasionally killing them in Guyana (though this observation may have involved the sister species C. orinocensis). Eggs and hatchlings are presumably vulnerable to the typical suite of nest predators.

Interestingly, many adults show evidence of healed injuries—missing toes, feet, or occasionally even the proboscis or head skin flaps. In Venezuela, piranhas sharing the same habitats may be responsible for such mutilations, though this has not been confirmed.

The mata mata does not hibernate or aestivate. Living in tropical lowlands with relatively stable year-round temperatures and water availability, it remains active throughout the year. Water levels in its habitat fluctuate seasonally with wet and dry seasons, but the species simply moves with changing water levels rather than entering dormancy.

The mata mata is an extreme dietary specialist, feeding almost exclusively on live fish. Rather than pursuing prey, it employs a remarkable ambush strategy: lying perfectly still on the bottom, camouflaged among leaf litter and debris, it waits for fish to approach. The numerous skin flaps on its head are heavily innervated and detect even slight water movements caused by nearby fish.

When prey comes within range, the mata mata strikes with explosive speed. It rapidly opens its massive mouth while simultaneously expanding the huge hyoid apparatus in its throat, creating powerful suction that pulls water—and the unfortunate fish—into its gaping maw. The whole sequence happens so fast that the prey has virtually no chance to escape. Fish up to 20–25 cm in length have been recorded as prey. In captivity, mata matas will eventually accept dead fish, though they initially prefer live prey.

Courtship behavior involves the male positioning himself in front of the female and repeatedly extending his head toward her while opening and closing his mouth. Movement of the lateral head flaps has been observed during these displays, along with exaggerated leg extension from the shell.

Nesting in the Amazon occurs from October through December. Unlike most Amazonian turtles that nest on open sandy beaches, mata matas select steep riverbanks of clayey sand or even excavate nests in decaying vegetation at forest edges. Females climb banks in a sideways fashion to negotiate steep grades. Nest sites are extremely difficult to locate, though indigenous peoples can find them with apparent ease.

Clutch sizes range from 12 to 28 eggs, with up to 32 recorded in captivity. The eggs are hard-shelled and nearly spherical, measuring 34–40 mm in diameter. Incubation is remarkably long—200 days or more in captivity, potentially quicker in the wild. Hatchlings emerge weighing 15–19 g with shell lengths around 49 mm.

The mata mata's most remarkable feature is its feeding mechanism—among the most specialized of any turtle. The combination of camouflage, sensory detection via innervated skin flaps, and explosive suction feeding makes it a supremely adapted ambush predator. When it strikes, the expansion of its massive hyoid apparatus creates such powerful suction that prey is essentially inhaled along with a rush of water.

The tubular snout is another remarkable adaptation, allowing the turtle to breathe while remaining almost completely submerged and motionless—only the tip of the snorkel breaks the surface. The tiny, anteriorly-placed eyes suggest that vision plays little role in prey detection; instead, the elaborate sensory flaps on the head and neck detect the vibrations of approaching fish, even in completely opaque water.

The mata mata has extremely poor swimming ability for an aquatic turtle, yet this apparent limitation suits its lifestyle perfectly. Rather than chasing prey, it simply waits—and its camouflage is so effective that it can remain virtually undetectable to both prey and predators.