In this doctoral thesis the most important characteristics of maritime transport in the Croatian part of the Adriatic are explored and analyzed by applying scientific methods, the newest international environmental requirements regarding prevention of pollution and its impact on shipowners are shown through the basic principle of the maritime market cyclic changes with guidelines for their adaptation (environmental friendly ship as an essential prerequisite for survival on the shipping market), and a global overview of available emission estimation methodologies is created and the possibilities of their application in the area analyzed. At the same time by a holistic approach to the problem various aspects of the impact of emissions from maritime transport to humans, the environment and climate are discussed. Taking the basic tenets of sustainable development and integrated coastal zone management into account, The Model of Emission Registry is set considering the specific characteristics of maritime transport in the Croatian part of the Adriatic that enables the creation of initial inventory of emissions (footprint) and their subsequent continuous monitoring on whose basis support for making and implementation of legislative decisions and economic instruments to protect the area of interest can be provided, which is also globally applicable to all similar areas. All relevant factors arising from the specifics of maritime traffic in the Croatian part of the Adriatic are researched on scientific basis, organizational (with regulatory, institutional, operational entities) and technological assumptions of the model are defined in relation to which the optimization of available assessment methodology was used to set up The Model of Emissions Registry that will result in more accurate data of emissions and, accordingly, provide better decision support and protection. So, the process of solving a defined scientific problem of insufficient study of atmospheric pollution from maritime traffic in the area observed is taken into account, and partly initiated, although the traffic is ever-increasing, and the development strategy of the Republic of Croatia is directed toward economy sectors directly related to the sea and the coastal area. The proposed model of the Emission Registry assumes the division of all vessels in the area in two separate groups to which then a different methodology can be applied in order to assess emissions and it enables the use of new technological solutions of maritime traffic monitoring, and the creation of an information system for monitoring and evaluation of emissions in maritime traffic based on dynamic analysis and mathematical models which will ensure more efficient control and the possibility of timely response in case of excessive pollution. The division into groups enables its development in phases which will possibly have as a consequence an extended period of consolidation of the results, but will certainly be easier to close the financial construction of the project that in this way can also be funded in phases from national sources as well as from various international sources. Finally, the proposed Model of Emission Registry also represents the basis for future scientific research in the field of prevention of pollution from maritime transport and its energy efficiency, one of which was presented to the project ASAP for whose continuity setting of the model is a prerequisite. In the same way once defined 'footprint' of emissions enables cost-benefit analyses in the field of maritime affairs as well as in other related scientific or economic areas. Consequently, it is concluded that the presented model of Exhaust Gases Emission Register in Maritime Traffic for Croatian part of the Adriatic is achievable and that in contrast to commonly separated methodologies for estimating emissions used globally, their partial application by distinctive and optimized groups, and subsequent integration of the results gives more accurate data of emissions that are taking specific characteristics of the study area into account.