Sonoyta mud turtles mostly feed on aquatic insects and snails that live on vegetation that grows in ponds and streams.  In habitats with poor aquatic invertebrate faunas, Sonoyta mud turtles shift to omnivorous feeding including plants and vertebrates that are available including mesquite tree pods and fish.

Sonoyta mud turtles are found in and out of water. These turtles require in-water aquatic habitat to survive in this otherwise extremely arid environment, so they are found in streams, as well as natural and artificial ponds that they use for feeding, to escape predators, to prevent their bodies from drying out and for mating. Sonoyta mud turtles also require terrestrial habitat, meaning out of the water, that maintains soil moisture. These areas occur along the banks of ponds and streams, and in intermittently dry sections of stream channels. Sonoyta mud turtles use these areas with moist soil to build nests that will keep their eggs from drying out. They also dig holes in areas with moist soil to keep from drying out when surface water disappears. While these turtles are pretty good climbers, they need accessible shoreline without too many vertical barriers so they can move between water and land.

Sonoyta mud turtles are active most of the year, except during times of drought when surface water almost disappears.  These turtles spend much of their time in water, feeding and basking, and males defend territories in water. Sonoyta mud turtles bask under root masses a few inches below water surface, on the water surface and on rocks along the Rio Sonoyta and Quitobaquito. Sonoyta mud turtles have the ability to close their shells nearly completely and can survive short periods without surface water by estivating, meaning that they go temporarily dormant, in terrestrial habitat or burying themselves in mud and remain in a stream or pond bed. Sonoyta mud turtles have been found in burrows up to 3.3 feet (1 meter) deep in stream banks, presumably using these burrows to escape from predators. Recent research efforts have also revealed that Sonoyta mud turtles are less likely to move along stream channels or away from water after disturbances when compared to the other subspecies of Sonora mud turtle.

The Sonoyta mud turtle is a moderate sized aquatic turtle that is oval in shape with a rough carapace, or top shell. These turtles are a bit bigger than a peanut M&M when they hatch and can grow up to 5.2 inches long (135 millimeters) by adulthood.

Sonoyta mud turtles have a olive-brown to dark brown carapace, or top shell. The plastron, or bottom shell, that is hinged front and back, and is yellow to streaked brown with dark seams. The head and neck are olive-gray with distinct stripes and reticulations. The digits on the feet are all webbed.

All turtle life histories are thought to be characterized, to varying degrees, by delayed maturity, meaning age at first reproduction, great longevity and repeated cycles of reproduction. The Sonoyta mud turtle follows this general paradigm.  

Sonoyta mud turtles usually live for approximately 10 to 12 years. The oldest Sonoyta mud turtle on record is a 39-year-old female found at Quitobaquito Springs, Arizona, in 2015.

Females leave the water to lay an average of four eggs in nests one to two times a year on land likely after mid-September. Embryo development takes about 80 days, but may be delayed until the following summer after they are laid. While this is common in the other subspecies, it is unknown with the Sonoyta mud turtle. Hatchling turtles are less than an inch in length. Hatchlings may then emerge and disperse from the nest to coincide with the onset of summer rains.  Females reach sexual maturity in six years or more and males reach sexual maturity in four to seven years. Sexually mature turtles are considered adults and females are usually larger than males. Mating occurs in the water.

The Sonoyta mud turtle is one of two subspecies of the Sonora mud turtle, and the other subspecies is called the Sonora mud turtle. The Sonoyta mud turtle is generally smaller than the nominate subspecies Sonora mud turtle. Not only do these turtles look very much alike, their names are similar, which adds to the confusion. However, the two subspecies do not overlap in range, so are not found in the same places. The Sonoyta mud turtle is found in a very small area along the international border between Arizona and Sonora, Mexico which is centered on the Rio Sonoyta drainage. The Sonora mud turtle, on the other hand, is found further to the east and north at distances at least 100 miles (161 kilometers) away. The Sonora mud turtle is more widely distributed throughout southeastern and central Arizona, into New Mexico and northern Sonora and Chihuahua, Mexico.