A capture unit for use with an antimicrobial application unit may include an upstream filter and a downstream filter. The upstream filter may be positioned to receive effluent from the application unit and to filter solid components from the effluent. The resultant upstream effluent filtrate may then be passed downstream to the downstream filter. The downstream filter may be used to filter an antimicrobial component from the upstream effluent filtrate and the resultant downstream effluent filtrate may be suitable for disposal as wastewater discharge. The antimicrobial is preferably a quaternary ammonium compound, is more preferably an alkylpyridinium chloride, and is most preferably cetylpyridinium chloride.