Five sites across the Kiel Fjord in the Baltic Sea (GEOMAR Pier: 54.330383 N 10.150683 E, Kiel Canal Entry: 54.361167 N, 10.162533 E, Falckenstein: 54.390217 N, 10.194983 E, Laboe: 54.405633 N, 10.209750 E, and Strande: 54.428267 N, 10.209267 E) were monitored biweekly from June 2013 until October 2020 (with some discontinuities in winter). Depth profiles were taken with a CTD (Sea & Sun Technology, Trappenkamp, CTD 60) recording temperature, salinity, pH, oxygen concentration as well as oxygen saturation. Oxygen and pH were corrected for temperature and salinity based on Standard Data Acquisition SSDA (C)opyright by SST 1999-2006. To avoid showing wrong measurements of the CTD probe, thresholds for the measured parameters were set (Temperature ≤ 25 °C, 8 ≤ Salinity ≥ 23, 5 ≤ pH ≥10, 0 mg L-1 ≤ Oxygen concentration ≥ 12 mg L-1 and 0% ≤ Oxygen Saturation ≥ 120%). Only those values were kept in the data set that did not exceed or fell below these thresholds. Furthermore, station specific depth limits were set (GEOMAR Pier ≤ 19 m, Kiel Canal Entry ≤ 13 m, Falckenstein ≤ 16 m, Laboe ≤ 17 m and Strande ≤ 17 m) and date exceeding of falling below these limits were excluded from the data set.