Constructed wetlands receiving treated wastewater (CWtw) are placed between wastewater treatment plants and receiving water bodies, under the perception that they increase water quality. A better understanding of the CWtw functioning is required to evaluate their real performance. To achieve this, in situ continuous monitoring of nitrate and ammonium concentrations with ion-selective electrodes (ISEs) can provide valuable information. However, this measurement needs precautions to be taken to produce good data quality, especially in areas with high effluent quality requirements. In order to study the functioning of a CWtw instrumented with six ISE probes, we have developed an appropriate methodology for probe management and data processing. It is based on an evaluation of performance in the laboratory and an adapted field protocol for calibration, data treatment and validation. The result is an operating protocol concerning an acceptable cleaning frequency of 2 weeks, a complementary calibration using CWtw water, a drift evaluation and the determination of limits of quantification (1 mgN/L for ammonium and 0.5 mgN/L for nitrate). An example of a 9-month validated dataset confirms that it is fundamental to include the technical limitations of the measuring equipment and set appropriate maintenance and calibration methodologies in order to ensure an accurate interpretation of data.