The Neuse River Estuary, North Carolina, USA, has demonstrated various symptoms of eutrophication during the past 20 years. The situation has stirred public opinion and political will to initiate programs to assess the problems and reduce nutrient loading. The Neuse River Modeling and Monitoring (ModMon) program represents such a program. The authors contributed to this program through ecological network analysis, a group of algorithms to evaluate networks of material flows within a structured system. Network analysis provided understanding of the relationship between nitrogen loading and recycling, the fates of loaded nitrogen and the expected inter-seasonal variation of both model inputs and ouputs. Some results show that recycling of loading nitrogen is very high, 90% or higher of total flow; one atom of nitrogen can be taken up by phytoplankton as much as 35 times; and there is little direct correlation between loading and productivity.