Abstract. Results of long-term measurements of CTD, current velocity, turbidity, and dissolved oxygen from three stations in the mouth of the Elbe Estuary in northern Germany are presented for the period of 2012 and 2013. The focus is on a station named HPA-Elbe 1, which is part of the COSYNA coastal observing system for northern and arctic seas, but data from two neighbouring stations are also presented for comparison and to bridge gaps in the time-series of HPA-Elbe 1. The variations of the variables exhibit distinct tidal patterns related to the longitudinal estuarine gradients of the water constituents and local sediment dynamics. On longer time-scales, spring-neap variability is observed, most prominently in the hydrodynamics. On the seasonal scale, the water temperature influences the degradation processes, which deplete the dissolved oxygen on the one hand and increase the oxygen contents by biological respiration on the other hand. Freshwater events from the catchment play an important role for sediment dynamics and mixing of riverine and coastal waters in the brackish water reach of the estuary. The periods of the deployment of the stations comprise the severest river flood observed so far in the Elbe in June 2013. The effects of the flood at the stations and along the estuary consist of a rapid flushing of the mixing zone and the turbidity maximum to the outer estuary and the transition to freshwater conditions from Hamburg to the mouth at Cuxhaven. The impact of the river flood at the stations is more pronounced in changes in salinity than in turbidity. The restoration of estuarine salinity and turbidity values comparable to those before the river flood took several months.