Description: This data set includes temperature and salinity measurements from 2019 and 2020 in the fjords Ameralik and Godthåbsfjord in southwest Greenland. Seasonal measurements were made at 12 standard stations in Ameralik spaced between 3 and 13 km from one another (AM1-12) in May, July and September 2019. Longer term fjord sampling was also carried out at monthly intervals from March to December 2019 at selected stations (AM3, AM5, AM7, AM10, AM11 and AM12) and March 2020 at station AM5. There was no sea-ice present in Ameralik during sampling. Additionally, sampling was conducted at 13 standard stations in Godthåbsfjord (GF1-13) in May, July and September 2019. In May and July, sea-ice in the inner part of the fjord prevented sampling further in-fjord. Favourable ice conditions during the September campaign allowed the sampling of 4 further standard stations (GF14-17). Longer term fjord sampling in Godthåbsfjord was also carried out at monthly intervals from February to December 2019 at selected stations from GF5 and inwards. All sampling took place on research vessels operating in daytime: the Greenland RV Sanna (May cruise), the commercial Greenland vessels Polar Dive (July cruise) and Tulu (September cruise), and the Greenland Avataq (remaining monthly day trips). At every station depth profiles of conductivity, temperature and pressure were collected using a SeaBird SBE19plus CTD and averaged over 1 m vertical depth intervals. Sensors were calibrated annually by the manufacturer and salinity precision was typically within the range of 0.005-0.010. Temperature (ITS-90) and practical salinity is used. The data have been used to describe the seasonal hydrography of Ameralik, impacted by a land-terminating glacier only, and to compare Ameralik with Godthåbsfjord, which receives meltwater from both land- and marine-terminating fjords.