Because the cover requirements of indigo snakes change seasonally, maintaining corridors that link the different habitats used is important. Burrows need to be in areas where there is no flooding. These piles are often destroyed for cosmetic reasons but should be left intact because they provide important hiding cover for both the snake and its prey. Humans represent the biggest threat to indigo snakes. Highway fatalities, wanton killings, and overcollection for the pet trade adversely affect indigo snake populations.
Indigo snakes are a commensal species associated with gopher tortoises.
For this reason it is necessary to maintain healthy tortoise populations, also a species in decline throughout its range. This is important because wild snakes seem to grow faster and produce more young than snakes held in captivity. Because smaller snakes do not use tortoise burrows, they should be released in wetland areas with plenty of herbaceous cover near the water's edge. Because hatchlings do not use tortoise burrows they may be susceptible to fire mortality. The absence of fire allows oaks to mature and leaf litter to accumulate, making burrow digging difficult and herbaceous food scarce.