The genesis of Hypoxia can be traced to nitrogen inputs from both natural (groundwater transport, riverine inflow and atmospheric deposition) and anthropegenic sources (sewage treatment plants, faulty septic systems, agricultural and lawn fertilizers and motorized vehicle emissions).
High nitrogen inputs spur rapid phytoplankton growth and periodic blooms that contribute to large organic loads. Bacterial decomposition of organic matter below the pycnocline (that usually forms during summer months) promotes oxygen depletion in the bottom waters. Hypoxia development is a cumulative process through the summer months corresponding to a period of thermally controlled stratification of estuarine waters. A highly stratified water column associated with the formation of the pycnocline exacerbates oxygen depletion because in prevents the mixing of surface and bottom waters. Hence, although the surface waters remain well oxygenated as a result of atmospheric and photosynthetic inputs of oxygen, bottom waters become progressively depleted in oxygen. This condition often spreads over extensive areas of the bottom until surface waters cool in the early fall, the density gradient declines and the pycnocline breaks down.