A syphon filtration system is a low head, small foot print, long operating cycle, gravity filtration system for treatment of water and wastewater, with one-stage or two-stage filtration in one vessel with different filtration media of sand, anthracite, granular activated carbon or other proprietary filtration media. The one-stage filtration system removes suspended solids or dissolved impurities and the two-stage filtration system removes suspended solids and dissolved impurities. In the two-stage filtration system, each filtration stage can be backwashed independently or both stages can be backwashed simultaneously. Novel syphon piping and controls design extend the filtration operating cycle and reduce the filter apparatus headroom, and the filter backwash water volume requirements.