We present a novel method for quantifying N₂ fixation by cyanobacteria, which is crucial in Baltic Sea eutrophication. Our Gas Equilibrium – Membrane-Inlet Mass Spectrometer (GE-MIMS), designed for operation on voluntary observing ships (VOSs), enables large-scale monitoring of surface water N₂ depletion caused by N₂ fixation. Laboratory tests confirm the device’s accuracy and precision, ensuring that it can complement current methods and contribute valuable data for better understanding N₂ fixation in the Baltic Sea.