The dataset comprises hydrographic observations collected during several cruises to Lake Grevelingen (The Netherlands) between 2022 and 2023 on board the R/V Navicula. The major aim in collecting CTD-data was to acquire information on the basic, sensor-based underlying physical and chemical conditions at the time of sampling, allowing an assessment of their spatial and temporal variability, as well as their role in controlling the biogeochemical cycling of several compounds (including climate-relevant trace gases). Data was collected by means of a SeaBird CTD system (SBE11) equipped with double sensors for temperature (SBE3), conductivity (SBE4), pressure (SBE9), oxygen (SBE43) and turbidity/fluorescence (FLNTU). . Data collection was carried out via a SeaBird Electronics deck unit using the Seasave software (version 7.26.7.107) software. Data processing was carried out by means of the Seasoft V2 software (https://www.seabird.com/software).