We report on a methodology for the direct potentiometric determination of nitrate in seawater by in-line coupling to an electrochemical desalination module. A microfluidic custom-fabricated thin layer flat cell allows one to electrochemically reduce the chloride concentration of seawater more than 100-fold, from 600 mM down to ∼2.8 mM. The desalinator operates by the exhaustive electrochemical plating of the halides from the thin layer sample onto a silver element as silver chloride, which is coupled to the transfer of the counter cations across a permselective ion-exchange membrane to an outer solution. As a consequence of suppressing the major interference of an ion-exchanger based membrane, the 80 μL desalinated sample plug is passed to a potentiometric flow cell of 13 μL volume. The potentiometric sensor is composed of an all-solid-state nitrate selective electrode based on lipophilic carbon nanotubes (f-MWCNTs) as an ion-to-electron transducer (slope of −58.9 mV dec–1, limit of detection of 5 × 10–7 M, and response time of 5 s in batch mode) and a miniaturized reference electrode. Nitrate is successfully determined in desalinated seawater using ion chromatography as the reference method. It is anticipated that this concept may form an attractive platform for in situ environmental analysis of a variety of ions that normally suffer from interference by the high saline level of seawater.