The construction and evaluation of a Low Temperature Co‐fired Ceramics (LTCC)‐based microsystem prototype as a possible on‐site microanalyzer to monitor the presence of two ions in water simultaneously is presented. The approach has been assayed to detect nitrate and chloride ions as model analytes by means of integrating in the same single substrate an ion selective polymeric membrane to nitrate and two screen‐printed Ag/AgCl electrodes. One supplies the chloride ion concentration and the other is to complete the potentiometric detection system as the reference electrode. The results obtained by the full characterization of the microanalyzer prove the relevance of the proposal and the possibility to be transferred to real‐world samples and environmental monitoring.