Since aquatic environments are highly heterogeneous and dynamic, there is the need in aquatic ecosystem monitoring to replace traditional approaches based on periodical sampling followed by laboratory analysis with new automated techniques that allow one to obtain monitoring data with high spatial and temporal resolution. We report here on a potentiometric sensing array based on polymeric membrane materials for the continuous monitoring of nutrients and chemical species relevant for the carbon cycle in freshwater ecosystems. The proposed setup operates autonomously, with measurement, calibration, fluidic control and acquisition triggers all integrated into a self-contained instrument. Experimental validation was performed on an automated monitoring platform on lake Greifensee (Switzerland) using potentiometric sensors selective for hydrogen ions, carbonate, calcium, nitrate and ammonium. Results from the field tests were compared with those obtained by traditional laboratory analysis. A linear correlation between calcium and nitrate activities measured with ISEs and relevant concentrations measured in the laboratory was found, with the slopes corresponding to apparent single ion activity coefficients γ(*)(Ca(2+)) = 0.55(SD = 0.1mM) and γ(*)(NO(3)(-)) = 0.75(SD = 4.7μm). Good correlation between pH values measured with ISE and CTD probes (SD = 0.2 pH) suggests adequate reliability of the methodology.