Pollutants, such as heavy metals, phosphorus, and pathogenic organisms, are removed from water by adding a chemical coagulant to water within an enclosure. With mixing, coagulation and flocculation occur, and a floc containing the pollutant settles to the enclosure bottom; so the treated water above the floc is free from at least some of the pollutant. Some of the treated water is removed from the enclosure, and new water is added. The new water and the settled floc are mixed to resuspend floc components. The process is repeated until the floc no longer exhibits contaminant-removal capability. In an alternate system, a matrix element is deployed within the enclosure, which captures a portion of the floc that settles within the water column. Pollutants in new water added to the enclosure encounter these suspended floc particles and are subsequently removed from the water.