A promising profiling setup for in situ measurements in lakes with potentiometric solid-contact ion-selective electrodes (SC-ISEs) and a data processing method for sensor calibration and drift correction are presented. The profiling setup consists of a logging system, which is equipped with a syringe sampler and sensors for the measurement of standard parameters including temperature, conductivity, oxygen and photosynthetically active radiation (PAR). The setup was expanded with SC-ISEs in galvanically separated amplifiers. The potential for high-resolution profiling is investigated by deploying the setup in the eutrophic Lake Rotsee (Lucerne, Switzerland), using two different designs of ammonium sensing SC-ISEs. Ammonium was chosen as a target analyte, since it is the most common reduced inorganic nitrogen species involved in various pathways of the nitrogen cycle and is therefore indicative of numerous biogeochemical processes that occur in lakes such as denitrification and primary production. One of the designs, which uses a composite carbon-nanotube–PVC-based membrane, suffered from sulfide poisoning in the deeper, sulfidic regions of the lake. In contrast, electrodes containing a plasticizer-free methacrylate copolymer-based sensing layer on top of a conducting polymer layer as a transducer did not show this poisoning effect. The syringe samples drawn during continuous profiling were utilized to calibrate the electrode response. Reaction hotspots and steep gradients of ammonium concentrations were identified on-site by monitoring the electrode potential online. Upon conversion to high-resolution concentration profiles, fine scale features between the calibration points were displayed, which would have been missed by conventional limnological sampling and subsequent laboratory analyses. Thus, the presented setup with SC-ISEs tuned to analytes of interest can facilitate the study of biogeochemical processes that occur at the centimeter scale.