The research presented in this manuscript concerns the evaluation of the effectiveness of microstrainers, which are designed to reduce the amount of plankton in treated surface water. The efficiency of microstrainer filtration analysis is very important for the proper course of the water-treatment process not only in the Water-Treatment Plant (WTP) in Zielona Góra (central western Poland) but also in other WTPs around the world. The qualitative and quantitative monitoring of the abundance of plankton including cyanobacteria during the particle-filtration process allows not only for the assessment of the potential cyanotoxic risk in surface water providing a source of drinking water, but also allows the evaluation of the action and the prevention of adverse impacts of microstrainers. Over four years of research, it was observed that the largest amount of cyanobacteria before microstrainer filtration took place in May. The dominant species was Limnothrix redeckei. The microstrainer removal of plankton and cyanobacteria was statistically significant. The quantity of removed plankton increased with its increasing content in raw water. The particle-filtration process, by reducing the amount of cyanobacteria, contributes to a decrease in intracellular microcystins.