The problems of environment and evaluation of natural capital belong to the phenomenology of externalities, and the requirements of environmental economics are ever more oriented towards the elaboration of the ecological–economic category of the externalization of internal expenses, wherefrom reasons for the introduction of ecological–economic instruments, before all payments for pollutions, ensue. Demystification of the negative conviction relating ecological payments as taxes is very important, since it must be shown that ecological payments correct, mitigate or remove externalities. Environmental protection is a complex system and it consists in a set of rules, measures and instruments that are applied for the surveillance of pollution sources, and shaping of instruments for environmental protection is a complex process intended for the accomplishment of established ecological goals. Among all instruments available for bridging the gap of internalization and exerting a significant effect on polluters to diminish their emissions of pollution, the ecological and economic ones are most important. The results of our investigation have demonstrated that it is necessary to reshape the current set of instruments regarding protection of vital functions of nature and an efficient environmental protection, and one of the key cognitions is that the scientific and professional public must not be excluded from the appraisals of creating and redesigning the instruments of environmental protection. These assertions have their foundation in the premise that the significance of elements of the social dimension in sustainable development is to a great extent determined by the level of environmental degradation and reduction in capacity of renewable sources. The paper, approach and data processing of the conducted research offer a new model and new elements of methodology for establishing the state and quality of the environment, whereby social-economic criteria of research (a socio–economic laboratory) are introduced into the fundamental analysis of the condition of crucial media of the environment, but also into shaping a more efficacious instrument set of protection. In such a way, a substantial contribution is given to the affirmation of a holistic and inter-disciplinary approach in the investigation and understanding the phenomenon of contemporary environmental reality, especially the central media of the environment (water, air, soil).