A new submersible probe for the in situ detection of nitrate, nitrite, and chloride in seawater is presented. Inline coupling of a desalination unit, an acidification unit, and a sensing flow cell containing all-solid-state membrane electrodes allows for the potentiometric detection of nitrate and nitrite after removal of the key interfering ions in seawater, chloride and hydroxide. Thus, the electrodes exhibited attractive analytical performances for the potentiometric detection of nitrate and nitrite in desalinated and acidified seawater: fast response time (t95 < 12 s), excellent stability (long-term drifts of <0.5 mV h−1), good reproducibility (calibration parameter deviation of <3%), and satisfactory accuracy (uncertainties <8%Diff compared to reference technique). The desalination cell, which can be repetitively used for about 30 times, may additionally be used as an exhaustive, and therefore calibration-free, electrochemical sensor for chloride and indirect salinity detection. The detection of these two parameters together with nitrate and nitrite may be useful for the correlation of relative changes in macronutrient levels with salinity cycles, which is of special interest in recessed coastal water bodies. The system is capable of autonomous operation during deployment, with routines for repetitive measurements (every 2 h), data storage and management, and computer visualization of the data in real time. In situ temporal profiles observed in the Arcachon Bay (France) showed valuable environmental information concerning tide-dependent cycles of nitrate and chloride levels in the lagoon, which are here observed for the first time using direct in situ measurements. The submersible probe based on membrane electrodes presented herein may facilitate the study of biogeochemical processes occurring in marine ecosystems by the direct monitoring of nitrate and nitrite levels, which are key chemical targets in coastal waters.