Within the context of 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. Due to a number of well documented and unusual atmospheric conditions, the early summer of 2013 in Central and Eastern Europe was colder and wetter than usual, with saturated soils, and higher than average cumulative precipitation. Additional precipitation at the end of May, and beginning of June, 2013, caused widespread floods within the Danube and Elbe Rivers, as well as billions of euros in damages. The floods generated the largest summer discharge on record within the last 140 years. The high-frequency monitoring network in the German Bight available within the Coastal Observing System for Northern and Arctic Seas (COSYNA) captured the flood influence on the German Bight. Monitoring 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 on the German Bight, which persisted for about 2 months after the peak discharge. The flood generated a large influx of nutrients, dissolved and particulate organic carbon on the coast. These conditions subsequently led to the onset of a chlorophyll bloom within the German Bight, 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 south eastern German Bight in the summer.