We present a new potentiometric sensor principle and a calibration protocol for in situ profiling of dissolved CO2 with high temporal and spatial resolution in fresh water lakes. The sensor system is based on the measurement of EMF between two solid-contact ion selective electrodes (SC-ISEs), a hydrogen ion selective and a carbonate selective sensor. Since it relies on SC-ISEs, it is insensitive to changes in pressure, thus suitable for in situ studies. Also, as it offers a response time (t(95%)) of <10 s, it allows for profiling applications at high spatial resolution. The proposed optimum in situ protocol accounts for the continuous drift and change in offset that remains a challenge during profiling in natural waters. The fast response resolves features that are usually missed by standard methods like the classical Severinghaus CO2 probe. In addition, the insensitivity of the presented setup to dissolved sulfide allows also for measurements in anoxic zones of eutrophic systems. Highly resolved CO2 concentration profiles obtained by the novel and robust SC-ISE setup along with the developed optimum in situ protocol allow investigating hotspots of biogeochemical processes, such as mineralization and primary production in the water column and help improving estimates for CO2 turnover in freshwater systems.