In the past few decades, scientists, policy-makers and concerned citizens have noted that increased development of coastal areas has led to deleterious changes in the nearshore waters. Many of these changes were traced to increases in the amount of nitrogen entering the waters (nitrogen loading) from changing uses of the adjacent land.

Investigators realized it would be necessary to understand the sources and pathways of nitrogen as it entered and traveled through a watershed on its way to a coastal embayment or estuary in order to determine how to control nitrogen inputs. With information from field studies, investigators began constructing mathematical models to help them understand and quantify the sources, pathways and fates of nitrogen derived from human activities. A mathematical model is a set of interrelated, inter-linked mathematical equations that computes the result of complex interactions among several variables. Building a mathematical model of the interaction of land use and coastal ecosystems requires an understanding of many different scientific disciplines, including biochemistry, biogeochemistry, hydrogeology, estuarine circulation, as well as many demographic features characteristic of the area under study. The power of computerized mathematical models is that they can perform simultaneous calculations of many interacting terms, to produce output that can be checked against "the real world", against actual observations, to see if the assumptions underlying our understanding of nature and how it works are correct. CLUE is a computerized mathematical model that summarizes our best understanding of how land use, nitrogen loading, and estuarine water and habitat quality are related. It allows exploration of various land use scenarios that differ in their effects on nitrogen loading, and on the consequences to water quality and marine life.