An improved system designed to control and filter runoff water in storm drains is presented. Drain water frequently carries trash, organic matter, suspended solids, hydrocarbons, metals, nutrients and bacteria collected from streets and parking lots into a storm drain inlet, which enters storm water drain pipe systems.The present invention supplies a series of baffle boxes inserted in the drain water stream with a final box possessing a selection from a collection of upflow filters, including a hydrocarbon-absorbing boom. The system can also support a storm flow bypass that directs high-flow storm runoff water directly to the outlet to protect the filter system.