The ocean’s methane emission to the atmosphere is dominated by continental shelves where cold seeps are globally common features. Seeps emit methane into the hydrosphere, but temporal variations and controls of seep activity and the efficiency of the microbial methane filter in the water column are scarce. Here we address this knowledge gaps by measuring whole water column methane inventories and methanotrophic activity at a temporal resolution of 226 hours at a North Sea cold seep (Doggerbank) in summer and autumn and also in the Dutch Wadden Sea.