A steady state budget for trace gases in the marine boundary layer is developed from a simple model of the marine boundary layer. Tracer balance is maintained in the marine boundary layer by five processes: (1) large-scale horizontal convergence of tracer, (2) pumping of tracer out of the marine boundary layer into the free troposphere by clouds, (3) penetration of tracer from the free troposphere into the marine boundary from compensating subsidence in the cloud free air surrounding cumulus clouds, (4) sea surface emission or deposition of the tracer, and (5) in situ photochemical production or loss of tracer within the marine boundary layer. The budget equation is used to derive an expression for the mixing ratio difference between the marine boundary layer and the free troposphere. Cumulus cloud mass flux is found to modulate all other processes that determine the mixing ratio difference between the two regions. A scale analysis indicates that the mixing ratio difference between the marine boundary layer and the free troposphere can be an order of magnitude smaller in disturbed weather conditions when compared with suppressed conditions showing that the difference in chemical concentrations between the free troposphere and the marine boundary layer cannot be rationalized solely on the basis of chemical measurements. The O3 measurements made during GAMETAG (Global Atmospheric Measurements Experiment on Tropospheric Aerosols and Gases) in the marine boundary layer are discussed in the context of the model. Finally, the analysis shows how sea surface emission rates of CH3I, CH3SCH3, H2S, and other reduced sulfur species can be estimated from measurement of the boundary layer-free troposphere concentration difference combined with measurements of the mass flux deduced from heat and moisture budget by using rawinsonde data. The approach is an alternate to the use of thin film models to estimate sea surface emission rates.