The present study aims to investigate the effect of aquaculture activity on the marine environment in a semi - enclosed bay at NE Aegean Sea, for the first time in scientific literature. The study was divided in three major thematic parts concerning structure and dynamics of macrobenthic communities, structure and dynamics of species trophic net and species geographic range size affinity as well as species biodiversity (a-,b-,γ- diversity, functional diversity) correspondingly. In this concept, the first thematic part included the investigation of benthic macrofauna response to the established environmental gradient, induced by the presence of an aquaculture unit, in a spatio-temporal scale. Spatial extent of aquaculture impacts on the marine environment was also detected whereas factors governing the magnitude of the impacts were also examined. The trophic net which is formed by benthic organisms was considered at the second thematic part as well as predators’ response to the environmental gradient. Concerning species zoogeography, variation of species geographical range size towards the environmental gradient was examined. A new methodology was also proposed concerning the assessment of environmental impacts in cases of disturbance which is based on species feeding and zoogeographical attributes. The third thematic part of this study targets to the investigation of macrobenthic biodiversity patterns (a-,b-,γ- diversity, Functional diversity) across the established environmental gradient by means of various diversity indices and theoretical approaches. The main results which occurred from this study revealed a severe modification of benthic communities’ structure and dynamics towards the most disturbed areas of the environmental gradient. Negative impacts of aquaculture activity were found to be restricted in a distance of fifty meters from the fish cages especially during summer and autumn. However, the environmental disturbance which was detected in the study area should not be attributed exclusively to the aquaculture activity. It was evident that the study area consist a deposit basin for the polluted sediments which are located in the central part of Gera’s Bay and which are arriving in the study area through the sediment transport paths of the Bay. Furthermore, endemic (local) species populations seemed to be gradually replaced by the more resilient populations of Boreal and Atlanto-Mediterranean species with increasing disturbance levels. The use of species feeding habits and species dispersal ability as indicators of disturbance effects proved to be a robust impact assessment technique since it was able to distinguish areas subjected to different levels of environmental stress in the study area. Investigation of diversity patterns in the study area revealed that the commonly used diversity indices weren’t sufficient for the comparison of the biocommunities. Macrobenthic functional diversity seemed to decline linearly with disturbance levels due to the loss of certain functionally important species across the environmental gradient. Rare species, which their vast majority was species with low dispersal ability and resistance, were found to vanish faster than other species and consequently to modify functional diversity levels in the study area.