A mobile floating water treatment system comprising a plurality of floating barges coupled together wherein one or more barges includes at least one baffle through which water passes for treatment purposes. The baffle may include includes a substrate material suitable for treating contaminated water. The baffle may be selectively raised from an interior tank of the barges in order to add or subtract substrate material. The substrate material may include at least one of calcium carbonate, silicon dioxide, cadmium and bismuth. The mobile floating water treatment system may also comprise a tugboat for mobilizing the barges and a dredge for collecting contaminated water and distributing the water to the barges. The water treatment system may include one or more vessel or railcar located adjacent said barges into which contaminants separated from said water may be diverted for storage, transportation and disposal.