A theoretical framework is developed for including cumulus cloud transport, rainout of water soluble gases, and aqueous phase chemistry into gas phase photochemical models. Cloud populations are represented as ensemble distributions of individual clouds of various heights. An individual cloud is represented as a one-dimensional, steady state plume with height independent radius entraining air from the boundary of the cloud. The model is applied to several hypothetical atmospheric tracers to show how clouds may affect the tropospheric distributions of ozone, NOy, SO2, PAN, hydrocarbons, and other gases. Although the numerical experiments were based on cloud mass fluxes from diagnostic studies in the tropics and thus are not representative of the entire globe, it was found that an increasing mixing ratio with height in the free troposphere can be produced for some gases with only a surface source when clouds are present. This suggests that some reactive troposhperic species with primarily surface sources may play a somewhat more important role in troposhperic chemistry than is presently believed depending on the global distribution of cloud mass fluxes. Deficiencies in existing photochemical models due to the way clouds are typically treated are discussed.