Data presented in this Ph.D thesis are results of a study performed in Boka Kotorska Bay (south Adriatic. During study period, hydrographic parameters and zooplankton were intensively sampled at seven fixed stations. Three of these stations were placed in the shallow part of the Bay near the shellfish farm, and four in the middle parts of each smaller bay that are part of Bay. Boka Kotorska Bay is a relatively closed part of the sea, with specific features such as the pronounced influence of surrounding land and an immense influx of fresh water. The special ecological conditions in Boka Kotorska Bay are reflected on taxonomic structure, distribution and abundance, both of individual species and the zooplankton as a whole. This thesis includes data on temperature, salinity regime, content and oxygen saturation percentage, concentration of pH ions, transparency and color of the sea. Temperatures oscillates both by months of the year and by depths of the sea. The surface temperatures increase from January to August and then decrease toward December. The thermocline starts to appear at depth of 0-15m in May and lasts till August. Later in autumn and winter slowly forms a uniform temperature, so the depth-induced differences are not significant. The temperature gradients ranged from 3.52ºC to 6.75ºC. The conclusion from these data is that the Bay is not a homogenous area in thermal sense.The salinity data clearly indicate the strong impact of fresh water impact on salinity, especially in the surface layer and the shallow habitats along the coast. The salinity values varied from 2.30‰ in September on the sea surface near the Institute to 38.00‰ in July at depth of 5 meters near Orahovac. This paper is the first to show data on salt balance in the Bay. Oxygen saturation over 100% affected all the layers from the surface to the bottom, indicating that the Bay was extremely well aerated and that it is an eutrophic area. These are the first data on degree of organic production in Boka Kotorska Bay and south Adriatic. These values reflect the degree of biological activity in the sea and its quantitative definition. The big amplitudes of basic hydrographic conditions of seawater in the Bay are the most important specificity factors of zooplankton fauna. Following zooplankton groups were determined and studied: Medusae, Siphonophorae, Cladocera, Copepoda, Pteropoda, Chaetognatha, Appendicularia (Larvacea), Polychaeta, Thaliacea and Larvae. Quantitatively most important are Copepoda, mostly species occurring throughout the year. Cladocera sharply increase the quantitative value of total zooplankton in summer months (number of individuals and volume of the sediments). The other groups are less represented and appear in certain periods of the year. We determined was a special alternation between typical neretic species and those from the open sea that spread their range to the waters of the Bay in a certain season and under characteristic ecological conditions. The regularity and periodicity of penetration of open-sea allochthonous species into the zone of coastal waters of the Bay was determined, and indicators of water mass movements were defined. Results of this paper include the biological monitoring at the Bay, based on following certain species within the zooplankton and the functional attributes of the ecosystem, plankton diversity and communities of zooplankton species. The combination of collected data were used to define the ecosystem of the Bay and to determine the degree of anthropic degradation within it.