Before CAP was constructed, many archaeological and biological studies were conducted by a number of local and federal organizations to determine how the environment would be affected by CAP and what could be done to minimize those affects. Planners realized many desert animals would be attracted to the canal for water, so in an effort to reduce animal drownings in the concrete-lined canal, a six-year study was conducted by the University of Arizona and a three-year study by the Arizona Game and Fish Department to identify ways of protecting wildlife along the canal route.

In addition, 15 major archaeological studies were completed and more than 5,000 historic and prehistoric sites were located. Of those, approximately 600 sites have or are currently being excavated. As a result of the biological studies and implementation of numerous features into the system, CAP successfully passed over 40 consultations with the federal government regarding the Endangered Species Act. The following are just a few of the ways CAP tried to mitigate its impact on the environment:

• Specially designed bridges were placed at important animal movement and migration paths so animals and desert tortoises can safely cross the canal.
• Eight-foot high fences line the canal on both sides to keep large animals safely out.
• The top five feet of the concrete lining have a rough finish to let small animals that get through the fence to climb down for a drink and safely back out.
• Funding was provided to the Arizona Game and Fish Department, Bureau of Land Management, Forest Service, National Park Service, and Pima County for construction of 45 wildlife watering sites located away from the canal.
• Construction near bald eagle nests was scheduled to avoid nesting season.
• Siphons and tunnels were constructed to solve the problem of crossing through flood plains, rivers, and mountains.
• With regard to desert vegetation, cacti and other native plants were salvaged and areas were re-vegetated to replace wildlife habitat disrupted by construction.