Microplastic (MP) contamination is becoming a significant challenge with the burgeoning use of plastic. The ubiquitous presence of the MPs in the sea (Baltic Sea) has raised care about their possible environmental impacts. Our research aims were to quantify the MPs accumulated in the open and coastal area environments, including water, sediments and biota. The potential impact of different land-based sources on marine biota was analysed. The amount, distribution, shape, color and polymer types of MPs in different matrices and the potential contribution of wastewater treatment plants (WWTP) and rivers to the MPs pollution in coastal areas were studied. The WWTPs can be considered as a main source of the MPs in the Estonian waters. There is an increase in the pollution level in the city with a higher population (Tallinn). Such sources as ports, rainwater, rivers flowing through the city and beaches also play an important role in the pollution of the sea with MPs. MPs were found in 24% of analysed benthic fish and just in 8% of pelagic fish. 43% of juvenile fish contained MPs vs 20.5% of adult fish. The most abundant polymer in fish guts was polyethylene.