The physical-biological interactions that affect the temporal variability of benthic oxygen fluxes were investigated to gain improved understanding of the factors that control these processes. This study, for the first time is able to resolve benthic diffusive boundary layer (DBL) dynamics using the newly developed lifetime-based laser induced fluorescence (τLIF) oxygen imaging system, which enables study of the role of small-scale fluid mechanics generated by benthic organism activity, and hence a more detailed analysis of oxygen transport mechanisms across the sediment-water interface (SWI). The net benthic oxygen flux across the sediment-water interface is controlled by sediment oxygen uptake and oxygen transport. While the oxygen transport is largely influenced by turbulence driven by large-scale flows, sediment oxygen uptake is mainly affected by oxygen production and biological- and chemical-oxygen degradation of organic matter. Both processes can be enhanced by the presence of fauna and are intimately coupled. The benthic oxygen flux can be influenced by fauna in two ways, i.e. by modulating the availability of oxygen, which enhances the sediment oxygen uptake, and by enhancing the transport of oxygen. In-situ and a series of laboratory measurements were conducted to estimate the short- and seasonal variability of benthic fluxes including the effects of burrow ventilation activity by tube-dwelling animals using eddy correlation (EC) and τLIF oxygen imaging techniques, respectively. The in-situ benthic oxygen fluxes showed high variability at hourly and seasonal timescales, where statistical analysis indicated that current velocity and water depth were the most significant predictors of benthic oxygen flux at the waterside, which co-varied with the discharge, temperature, and oxygen concentration. The range of variability of seasonal fluxes corresponded to the friction velocities which were driven by large-scale flows. Application of a simplified analytical model that couples the effect of hydrodynamic forcing of the diffusive boundary layer with a temperature-dependent oxygen consumption rate within the sediment showed that friction velocity and temperature cause similar variability of the steady-state benthic oxygen flux. The application of τLIF oxygen imaging system in bioturbation experiments enabled the investigation and discovery of insights into oxygen transport mechanisms across the sediment-water interface. Distinct oxygen structures above burrow openings were revealed, these were associated with burrow ventilation. The DBL was degraded in the presence of burrow ventilation. Advective transport generated by the energetic plumes released at burrow outlets was the dominant transport driving mechanism. The contribution of diffusive flux to the total estimated decreased with increasing larval density. For a range of larvae densities, commonly observed in ponds and lakes, sediment oxygen uptake rates increased up to 2.5-fold in the presence of tube-dwelling animals, and the oxygen transport rate exceeded chironomid respiration by up to a factor of 4. The coupled physical-biological factors affecting net benthic oxygen flux can be represented by temperature, which is a prominent factor that accounts for both oxygen transport and sediment oxygen uptake. Low oxygen transport by flow coincided with high summer temperatures, amplified by a reduction of benthic population density and pupation. It can also, however, be offset by increased ventilation activity. In contrast, low temperature coincided with high oxygen concentrations, an abundance of larvae, and higher flow is offset by less burrow ventilation activity. Investigation of the effect of hydrodynamics on oxygen transport alone suggested that the expected increase of benthic oxygen flux under global warming can be offset by a reduction in flow velocity, which could ultimately lead to increasing carbon burial rates, and in a growing importance of anaerobic mineralization pathways with increasing emission rates of methane. This study suggests a significant contribution of biological induced benthic oxygen flux to physical transport driven by large-scale flow-fields contributing to bottom-boundary layer turbulence.