We report on a novel approach for in-line sample acidification that results in a significant improvement of the limit of detection of potentiometric anion-selective electrodes aiming at determining nutrients in natural waters. The working principle of the developed acidification module relies on the cation-exchange process between the sample and an ion-exchange Donnan exclusion membrane in its protonated form. The resulting in-line acidification of natural waters with millimolar sodium chloride level (freshwater, drinking water, aquarium water as well as dechloridized seawater) decreases the pH down to ~5. By using the acidification module the limit of detection of nitrite-selective electrodes significantly improves by more than 2 orders of magnitude with respect to that observed at environmental pH. The originality of the proposed flow cell lies in the possibility to adjust the pH of the sample by modifying its exposure time with the membrane by varying the volumetric flow rate. Facile coupling with a detection technique of choice, miniaturized configuration and simple implementation for long-term monitoring with submersible probes for environmental analysis are possible analytical configurations. This approach was here successfully applied for the potentiometric detection of nitrite in aquarium and dechloridized seawater samples.