Cyanobacteria are a potential threat to aquatic ecosystems and human health because of their ability to produce cyanotoxins, such as microcystins (MCs). MCs are regularly monitored in fresh waters, but rarely in estuarine and marine waters despite the possibility of their downstream export. Over a period of two years, we monthly analyzed intracellular (in phytoplankton) and extracellular (dissolved in water) MCs at five stations along a river continuum from a freshwater reservoir with ongoing cyanobacterial blooms to the coast of Brittany, France. MCs were quantified using two integrative samplers placed at each site: solid phase adsorption toxin tracking (SPATT) samplers for collecting extracellular MCs and caged mussels (Anodonta anatina and Mytilus edulis) filter-feeding on MC-producing cyanobacteria. The MC transfer was demonstrated each year during five months at estuarine sites and sporadically at the marine outlet. SPATT samplers integrated extracellular MCs, notably at low environmental concentrations (0.2 µg/L) and with the same variant profile as in water. The mussel A. anatina highlighted the presence of MCs including at intracellular concentrations below 1 µg/L. M. edulis more efficiently revealed the MC transfer at estuarine sites than water samplings. Bivalves showed the same MC variant profile as phytoplankton samples, but with differential accumulation capacities between the variants and the two species. Using SPATT or bivalves can give a more accurate assessment of the contamination level of a freshwater-marine continuum, in which the MC transfer can be episodic. MC content in M. edulis represents a potent threat to human health if considering updated French guideline values, and particularly the total (free and protein-bound) MC content, highlighting the necessity to include cyanotoxins in the monitoring of seafood originating from estuarine areas.