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Eutrophication process is a serious problem in water ecosystems. There is a great need to study the relation between the physico-chemical condition of water and the influence of these parameters on the diversity of biological life, especially on changes in the structure of microbiocenoses. The most interesting are bacteria and microalgae, due to the important roles they play in maintaining the balance of the aquatic environment. In this study, biodiversity analysis of eukaryotic microalgae and bacteria in two artificial water ecosystems - fish farming ponds - was performed. Aquaculture was based on IMTA technology, in which every part of the trophic chain plays a significant role in maintaining the balance in the ecosystems. Experimental intensive - extensive systems differed in terms of nutrient loads, ponds were characterized by high loads of organic and inorganic nitrogen and phosphorus. During the experimental period, the physicochemical conditions, quantitative genotypic structure of the two biocenoses being studied and the relation between these factors were monitored and investigated. For the biodiversity analysis, the PCR - DGGE technique was used. The results of preliminary research showed that there is a correlation between nutrient loads, diversity expressed in the Shannon-Wiener Index and the overall condition of experimental systems. Higher loadings of nutrient promote the development of bacteria and microalgae without any influence on the balance in the artificial ecosystem being tested.