Cyanobacterial proliferations display rapid spatiotemporal variations that can interfere in the assessment of water contamination levels by microcystins (MC), and make necessary the use of integrative tools. This study evaluates the pertinence of bivalves Anodonta anatina and Dreissena polymorpha as bioindicators of the presence of MC-producing cyanobacteria in water. Ingested MC accumulates into two fractions in bivalve tissues—the cellular free and the protein-bound fractions—both forming the total MC fraction. Mussels were exposed to the cyanobacteria Planktothrix agardhii at densities producing an equivalent of 1, 10 and 100 µg/L of intracellular MC, with the evaluation of: (i) cyanobacterial cells and MC daily intake by mussels, (ii) free and total MC kinetics in whole individuals (using all the tissues) or only in the digestive gland, during and after the exposure, (iii) bioaccumulation factors. For each species, the kinetics of the two accumulation fractions were compared to evaluate which one best reflect levels and dynamics of MC-producing cyanobacteria in water. Results showed that the dynamic of free MC in bivalve tissues better highlight the dynamic of intracellular MC in water. Using whole D. polymorpha may be appropriate to reveal and discriminate the water contamination levels above densities of cyanobacteria producing 1 µg MC/L. Digestive glands of A. anatina appeared more sensitive to reveal low environmental concentration, but without direct correlation with levels of water contamination. Further experimentations in situ are necessary to confirm those results in order to propose the use of freshwater bivalves for a biomonitoring of MC-producing cyanobacteria in fresh waters.