Biogeochemical processes are often confined to very narrow zones in aquatic systems. Therefore, highly resolved in situ measurements are required to study these processes. Potentiometric solid-contact ion selective electrodes (SC-ISEs) are promising tools for such measurements. SCISEs show good performance in analyses under controlled experimental conditions. Very few sensor designs, however, can sustain the challenges of natural water matrices and external environmental conditions during in situ applications. We fabricated ammonium and pH selective SC-ISEs with functionalized multiwalled carbon nanotubes (f-MWCNT) as a solid contact. Their functionality was tested in the laboratory and applied in situ for vertical profiling in a eutrophic lake. Sensors were insensitive to strong redox changes, high sulfide concentrations, and bright daylight conditions during the application in the lake. In addition, sensors are easily fabricated and exhibit short response times (<10 s). The proposed design of SC-ISEs based on f-MWCNTs is quite suitable for high-resolution in situ profiling of ionic species in fresh water lakes.