The concept of eco-efficiency has recently become an issue of great importance due to the growing trend of environmental degradation, and many approaches based on Data Envelopment Analysis (DEA) are used in the literature to evaluate the environmental performance of economic systems. However, research to date has paid little attention to the possibility of extending the DEA approach to the problem of measuring the economic feasibility of eco-efficiency improvement. The main aim of this study is to evaluate the efficiency of investments focused on improving the eco-efficiency of the regional economy in Russia using the DEA approach. The various types of costs for environmental protection measures are considered as inputs and the annual decrease in specific environmental impacts of the regional economy are considered as outputs of DEA models. This is different from previous research, which generally focused on environmental efficiency only, omitting the integration of economic aspects in eco-efficiency measures. This study compares three different modifications of basic DEA models in the context of technical complexity and practical feasibility. The results show that the efficiency of regional environmental management in many Russian regions has a great potential for improvement. From a practical point of view, the Slack-Based Measure (SBM) model provides the most accurate results for policy applications. Unlike other ratings, the DEA-SBM model may stimulate an optimization of environmental protection spending and the introduction of technological and organizational eco-innovations.