The scientists said the wall would alter the movement and "connectivity" of wildlife and the animals' potential isolation might be a threat to populations of some species.
But the researchers said technology and design alterations could dramatically improve the potential for animals to move more freely between the two countries.
Oregon State University Assistant Professor Clinton Epps and University of Arizona biologist Aaron Flesch looked at the potential effects of the security wall on two species -- the pygmy owl and bighorn sheep.
They found some of the potential damage to low-flying pygmy owls could be mitigated by erecting poles near the fence to allow the owls to swoop from a perch, and planting brush to provide better cover to help them avoid predation, Epps said.
The security wall could have a bigger impact on the movement of bighorn sheep, isolating populations and potentially reducing their genetic diversity. But the scientists say a virtual fence in some areas would allow the sheep to travel, especially in steep terrain.
The researchers said other animals might also be affected by the security wall, such as black bears, jaguars, pronghorn antelope, desert tortoises and ground-dwelling birds.
The study appeared in the journal Conservation Biology.