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 knowledge on variations and controls of seep activity and the efficiency of the microbial methane filter in the water column is scarce. Here we address this knowledge gap by measuring whole water column methane inventories and methanotrophic activity at a temporal resolution of 2 hours at a North Sea cold seep (Doggerbank) in summer and autumn. We found that methane inventories were 40% higher at low tide compared to high tide concurrent with an elevated activity of methanotrophs. The activity of methanotrophs was reduced during autumn when the water column was fully mixed and matched by higher methane emissions to the atmosphere. Our results show that tides are underappreciated controls on seepage, methanotrophic activity and sea–atmosphere fluxes.