Abstract: Several processing protocols were systematically investigated for the preparation of dissolved microcystins (MCs) samples. Some key parameters affecting toxin determinations in sample preparation process were further identified and quantified. We evaluate the influence of five different filters on the preparation of MCs samples. Results indicated that nearly 79% of added MCs could be absorbed by some membranes like CA filter for the filtration, which lead to the significant underestimation of MCs risks associated with toxin contaminations. Meanwhile, GF/C filter and PES filter tip are suitable for the preparation of dissolved MCs samples. In addition, centrifugation with the aim of removing algal cells also has significant impact on dissolved MCs determination. Results from this study will provide important information on the determination of dissolved microcystins and further lead to the standardization of the extracellular toxin determinations in risk assessments.