This paper suggests an approach to evaluating the efficiency of regional ecologic management systems based on the basic Data Envelopment Analysis (DEA) models. An advantage of this approach is the possibility to identify best environmental protection practices, calculate the volume of ineffective expenditure, and find (and further use in planning) target indicators for decrease in negative ecologic effects of the regional economy. This approach was tested on the Southern Federal district of Russia, which is a macro-region with a high anthropogenic load. Using the suggested approach in the regional ecologic management practice will allow to improve managerial decisions and increase the transparency of environmental protection activity.