The Calvi Bay is a low-runoff system located on the western coast of Corsica. It opens to the north to the Ligurian Sea, one of the main sub-basins of the Northwestern Mediterranean Sea. This dataset contains long-term time series (2012 - 2020) of high-performance liquid chromatography (HPLC) phytoplankton pigment concentrations measured at the Canyon head station, a station located in the outer part of the Calvi Bay. The pigments measured (in ng L-1) include: chlorophyll a (chl a), divinyl chlorophyll a (DVchl a), total chlorophyll a (Tchl a), peridinin (Peri), 19'-butanoyloxyfucoxanthin (Buta), fucoxanthin (Fuco), neoxanthin (Neo), prasinoxanthin (Prasino), violaxanthin (Viola), 19'-hexanoyloxyfucoxanthin (19’HF), alloxanthin (Allo), zeaxanthin (Zea), lutein (Lutein) and total chlorophyll b (Tchl b). Sampling and analysis methods are described in Goffart et al. (2015). These data are used to calibrate and validate ocean color remote sensing algorithms and to infer phytoplankton functional types using machine learning approaches.