This dataset was collected during the cruise MSM129/1 with RV MARIA S. MERIAN from Warnemünde, Germany to St. John's, Canada. It contains chlorophyll-a measurements [µg/l] from water samples collected from the seawater supply (Reinseewassersystem, RSWS) as well as from three CTD casts to calibrate the fluorometers of the RSWS system and the CTD, respectively. The outflow of a PocketFerrybox that was connected to the seawater supply in the hangar was used for sampling. It takes a substantial amount of time for the water to reach the hanger from the intake point. The time delay between the sensor readings of the RSWS and the PocketFerrybox was determined and the timestamps of the water sampling were adjusted accordingly. Given latitute and longitude refer to this corrected timestamp. The original time of water sampling in the hangar is given as an additional column with the comment time of sampling. To obtain chl-a concentrations, water samples were filtered onboard through 0.7 μm pore size, glass fiber filters (Whatmann GF/F) under low vacuum. Filters were frozen immediately at -80 °C until extraction in laboratory by 90% acetone method. Concentrations were calculated from fluorescence measured with a pre-calibrated Turner Design TD 7200-02 laboratory fluorometer (EPA445.0, Turner Manual).