At 715 km long, the Susquehanna River is the longest river on the east coast of the United States. The river originates at Otsego Lake in New York State and drains 71,225 km² in New York, Pennsylvania and Maryland before emptying into the Chesapeake Bay. Much of the impetus for surface water quality protection in the river basin arises from the presence of the Chesapeake Bay where it is now generally recognized that water quality problems are caused by nutrients transported to the Bay in its tributary rivers from both point and non-point sources. The amounts of nutrients coming from non-point sources reflect land management and farming practices and are of particular significance for the Chesapeake Bay, because the land-area/water volume ratio is far higher than any other riverine estuary in the world. The physiography and hydrology of the Susquehanna River basin, which is comprised of portions of glaciated and unglaciated Allegheny Plateau, Valley and Ridge, Piedmont, and Coastal Plain provinces, plays a key role in how agricultural lands are managed and also plays a determinative role in nutrient transport from agricultural soils to water. Water quality research emphasizes phosphorus sources, losses, and transformations associated with runoff and stream transport, understanding the basic N relationships and balances within the watershed, identifying and quantifying the primary nitrogen source and sink zones, and using chemical data to identify hydrologic source-areas, generalized flow pathways, and zones where degradative chemical processes occur. In addition to agricultural impacts on water quality in the Susquehanna River basin, other sources of impairment include mining, urbanization and atmospheric deposition.