Decomposition of incorrectly disposed or unmanaged polymer waste in the environment is a long-term process with unwanted and worrying products. In this way, climatic influences enable weakening of physical and chemical properties of plastic material but also its decay, which in turn opens the possibility of migration by air or water to living organisms. Such particles, whose exact risk is still unknown and of great concern, are called microplastics (MP). They are categorized as polymer particles smaller than 5 mm in size. The main focus so far has been on ecotoxicological research, but now also on trying to design an alternative system for bioremediation of the main components of the environment in order to protect the ecosystems against potential adverse effects. The aim of this study was to biodegrade polystyrene and polyvinyl chloride MP by use of Pseudomonas alcaligenes bacterial culture in an aquatic environment and to record the potential adverse effects of unknown metabolites that may occur. A Full factorial design was applied to set up a three-factor experiment on three levels. The main factors in the PS experiment were particle size, number of revolutions, and optical density (OG) and with PVC there were pH value, MP concentration and optical density (OG). The experiment was conducted for 30 days and samples were taken on the 0., 3., 7., 14., 21. and 30. day. In aformentioned days we monitored the concentration of organic and inorganic carbon, OG, CFU and by-products formation with HPLC-MS analysis. Analysis of changes in the PS and PVC particle structure after the experiment was carried out by FTIR-ATR spectroscopy and the toxicity of the filtrate was determined by use of bacteria V. fischeri. All the aforementioned analyzes confirmed that the process actually causes changes in the structure of the plastic, which indicates that it biodegrades. Analysis of variance (ANOVA) confirmed that the model is significant in both experiments and that the optimal conditions for conducting experiments with PS are: number of revolutions of 180 rpm, MP size 203 μm and OG 0,27. In the experiment with PVC, the ideal conditions are pH 7, γMP 50 mg/L and OG 0,3.