This master thesis focuses on microplastic sampling in the Ljubljanica River and Lake Bled using three different methods through the entire water column. We have developed and tested the sampling methodology by a petrol water pump through the water column for assessing microplastic and mesoplastic concentrations. Waste legislation and regulations in Slovenia and in Europe, the main properties of plastic, the impact of plastic waste on the water environment and the impact of plastic and microplastics on the ecosystem and on humans have also been discussed. 38 samples were gathered using three sampling methods: a) surface – epi-neuston net, b) between the surface and the bottom – petrol water pump, c) sediment – Van Veen grab. The samples were examined thoroughly in a laboratory by two different methods according to the sampling method. Microplastics or mesoplastics were separated from the samples. Microplastic or mesoplastic sampling results obtained throughtout the methods used in sampling in the Ljubljanica River and Lake Bled were first compared separately. Furtheron, the results of the sampling methods between the Ljubljanica and Lake Bled were analysed. We have found out that microplastics can be identified in the Ljubljanica as well as in Lake Bled through the entire water column, mostly on the surface. On the basis of the results of this research, it can be concluded that microplastics are already present in Slovenian watercourses as well as in lakes which leads to potential ecological problems. The results show that a petrol water pump and its sampling methodology through the water column is more suitable for microplastic sampling in lakes than in watercourses. The comparison of the microplastic sampling results obtained by an epineuston net in the Ljubljanica and Lake Bled with the sampling results in certain watercourses and lakes around the world demonstrates that the results obtained in Slovenia are comparable to the ones around the world.