Within the context of the predicted and observed increase in droughts and floods with climate change, large summer floods are likely to become more frequent. These extreme events can alter typical biogeochemical patterns in coastal systems. The extreme Elbe River flood in June 2013 not only caused major damages in several European countries but also generated large-scale biogeochemical changes in the Elbe estuary and the adjacent German Bight. The high-frequency monitoring network within the Coastal Observing System for Northern and Arctic Seas (COSYNA) captured the flood influence on the German Bight. Data from a FerryBox station in the Elbe estuary (Cuxhaven) and from a FerryBox platform aboard the M/V Funny Girl ferry (traveling between Büsum and Helgoland) documented the salinity changes in the German Bight, which persisted for about 2 months after the peak discharge. The Elbe flood generated a large influx of nutrients and dissolved and particulate organic carbon on the coast. These conditions subsequently led to the onset of a phytoplankton bloom, observed by dissolved oxygen supersaturation, and higher than usual pH in surface coastal waters. The prolonged stratification also led to widespread bottom water dissolved oxygen depletion, unusual for the southeastern German Bight in the summer.