The disclosed methods and systems of water purification relate to burying an underdrain in situ under a filter media bed such as a particulate material bed, within a natural body of water. A pump is provided for withdrawing water from the underdrain at a sufficient rate to cause a complex biological matrix filter to proliferate on top of the filter media bed forming a portion of the floor of the body of the water. The filter media bed is positioned at a depth d of water between the water body surface and the water body floor so that the upper surface of the particulate material bed remains substantially undisturbed by wave motion or tidal action at the surface of the body of water to facilitate the proliferation of the biological matrix filter.