In situ methane emission measurements from sediments are combined with water column backscatter anomalies recorded with an Acoustic Doppler Current Profiler (ADCP) integrated on a benthic observatory. During cruise SO191 to the Hikurangi Margin (New Zealand), the Fluid Flux Observatory (FLUFO) was deployed at a cold seep site at Omakere Ridge. The sediments incubated in the two benthic chambers of FLUFO contained seep-associated fauna, including small and larger tubeworms, juvenile bivalves of the genus Acharax and some juvenile clams. The first 26 h of in situ incubation revealed low to moderate methane fluxes of 0.01 to 0.4 mmol m − 2 d − 1 into the overlying water of the backup and flux chamber, respectively. In the following sampling sequence, however, the methane concentration in the flux chamber reached 3-fold higher concentrations whereas the methane concentration in the backup chamber remained low and unchanged. Simultaneous to the sudden methane increase, a significant backscatter anomaly was recorded and persisted for 30 min and covered the entire depth range (100 m) of the upward looking ADCP. Data analyses revealed that a single-phase plume (no bubbles) outburst likely occurred during this time. While bubbles appeared to be present during some periods, plume simulations revealed that the volume of gas required (rate of 8 ton/day) does not support a bubble plume. A second data set was obtained during lander deployments at Rock Garden where visual observations by ROV confirmed the transient pattern of free gas injection into the water column. Acoustic flares and methane concentration increase in the bottom water hint towards a pressure (tidal) induced discharge mechanism. The presented data demonstrate the temporal and spatial variability of seabed methane emission, and very short methane signal lifetime in the water column (hours to a few days) due to turbulent diffusion. Both have to be considered when methane budgets are extrapolated from single methane emission rates.