Hydrographic and current time series data from Isfjorden online mooring (IFO) during 30 September 2016 to 11 March 2017 at 78°14.845’ N; 015°19.870’ E, and 60 m depth. The mooring was deployed by the University Centre in Svalbard (UNIS) in collaboration with Aanderaa Data Instruments (AADI) as part of the Svalbard Environmental Protection Fund project “Blir det is på Isfjorden i år?” to monitor inflow of Atlantic Water to Isfjorden and possible presence of sea ice on the surface. IFO constituted of an Aanderaa Instruments recording Doppler current profiler (SeaGuard II) configured with 2-m bins and with auxiliary CTD sensors, and was deployed on 30 September 2016 in a bottom frame at 60 m depth. On 3 November 2016, a 40 m SeaGuard string with temperature and conductivity sensors at 46 m and 33 m depths was connected to the SeaGuard II and ended in an in-line SeaGuard with auxiliary CTD sensors at 20 m depth. The sea cable providing power to the instruments and transferring data to land, was cut off on 11 March 2017. For further details of the mooring and data, see Skogseth et al. (2019).