While transfer of freshwater cyanobacteria to estuaries has been observed worldwide, the associated transfer of cyanotoxins is less often reported, in particular the sediment contribution. During fall 2018, we monitored the co-occurrence of cyanobacteria and microcystin (MC) in both the water column and in surface sediments at five stations along a river continuum, from a freshwater reservoir to the coastal area in Brittany, France. Cyanobacteria dominated the phytoplankton community in the water column with high densities at the freshwater sites. Microcystis cells and intracellular MC transfer to estuarine and marine sites were observed with decreasing concentrations in accordance with flow dilution. Extracellular MC showed the opposite trend and increased from upstream to downstream in accordance with the lysing of the cells at elevated salinities. Surface sediment samples contained high densities of colonial Microcystis in freshwater and with decreasing concentrations along the salinity gradient, similar to cells concentrations in the water column. Intracellular MC was detected in sediment at all sites except at the marine outlet suggesting the survival of intact cells. Extracellular MC concentrations in sediment were up to five times higher than intracellular concentrations suggesting incomplete MC degradation. mcyB genes were present at all sites, while mcyA genes were absent at the marine outlet suggesting the presence of toxic strains along the estuary. The high densities of intact colonies of potentially toxic Microcystis in the estuarine sediment strongly suggest that sediments can act as an inoculum of cyanobacteria and cyanotoxins in estuaries.