Dataset containing hydrographic and biogeochemical data from two fjords (Godhäbsfjord and Ameralik Fjord) in southwest Greenland. Data was collected during expeditions in July 2018 (KQ2018) and September 2019 (TU2019), as part of ERC funded (678371) project ICY-LAB (Isotope CYcling in the LABrador Sea) and Royal Society funded (RGF\EA\181036) project Biogeochemical Cycling in Greenlandic Fjords. All data derived from sensors are reported as an average related to the sampling period for the laboratory analysed data. For data corresponding with Towfish samples, this is a time-averaged value, corresponding to the time the Towfish was in the water and sampling occurred. For Niskin derived samples, the average for sensor derived data was calculated from a 5m depth window from a depth profiler CTD. Sampling method refers to the method in water samples were collected, prior to filtration, storage and laboratory analysis. FISH = a Towfish that was deployed for surface (up to 5m, average 3m) sampling. All detailed sampling protocols and station descriptions can be found in the associated cruise reports.