Onondaga Lake, located in Syracuse, New York, has been considered one of the most polluted lakes in the world. One of the major problems due to excess nutrients and productivity is the development of an anoxic layer in the lower depths of the water column during the summer months. It is relatively accepted that this lack of oxygen is due to sinking algal matter and other forms of particulate matter being degraded by bacteria, however my research focuses on which form of detritus plays the largest role in the development and growth of this anoxic layer. By isolating fatty acids and sterols from phytoplankton and POM from different depths in the lake, I have been able to determine which species are present, how they are being degraded by bacteria, and compare this to the changing oxygen levels over the course of the summer. By determining the relative amounts of diatom biomarkers 16:1w7, 20:5w3, and 24-methylcholesta-5,22-dien-3b-ol from seston samples from several depths in June, it was hypothesized that an early spring diatom bloom was present followed by subsequent sinking into the lower water column. By measuring the bacterial productivity and oxygen levels in each layer, it was concluded that the breakdown of sinking diatoms by bacteria has a significant affect on the setup of anoxia. Several other freshwater lakes develop low levels of oxygen in their bottom layers and through studying Onondaga Lake, it is expected that these methods can be employed to lessen this problem in many bodies of water.