A system and method for applying a protective layer to a cotton module of compacted cotton moving in an unloading direction from a cotton module builder through an open end thereof along an unloading surface, the system including application apparatus having at least one applicator in fluid communication with at least one tank for applying a fluid contained in the at least one tank to at least a top surface of the cotton module, the fluid being applied to an exterior of the cotton module in a fluid state and solidifying into a water resistant layer prior to significantly permeating the exterior of the module, so as to capable of being removed therefrom prior to processing of the module.