In 1991, the USGS began to implement a full-scale NAWQA Program. The three major objectives of the NAWQA Program are to provide a consistent description of current water-quality conditions for a large part of the Nation's water resources, to define long-term trends (or lack of trends) in water quality, and to identify, describe, and explain the major factors that affect observed water-quality conditions and trends. These objectives are being met (1) by conducting retrospective analyses of existing data, (2) by establishing a long-term nationwide monitoring network designed to assess existing water-quality conditions and provide a data base for trend analyses, and (3) by conducting process-oriented studies designed to provide a better understanding of the relation between land-and water-use activities and water-quality conditions. The NAWQA Program is providing an improved scientific basis for evaluating the effectiveness of water-quality management programs and practices.The NAWQA Program is being implemented through investigations of hydrologic systems in 60 study units that include parts of most major river basins and aquifer systems in the United States. Study units range in size from 1,200 to about 65,000 mi2 and incorporate 60 to 70 percent of the Nation's water use and population served by public water supply. The south Florida study unit includes most of the southern half of the Florida Peninsula and contains a major urban complex of more than 5 million people. The study unit in this report was included in the NAWQA Program in 1993.

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We present a new concept and techniques for processing flow and salinity data and calibrating a box model designed to estimate water residence times in Charlotte Harbor, a large estuary in southwestern Florida. The new concept is that, over many tidal cycles, the tidally averaged “flow” (Qg) of water from the Gulf of Mexico with a salinity of 35‰ can be treated as a constant at any point in the estuary. This flow is used in a simple mixing equation to predict salinity in the estuary at different river inflows, and the predicted salinities are used to compute residence times for water in the estuary. The techniques developed to achieve optimal precision in the relation between river inflow and salinity include a newly derived equation to fit Qg by a least‐squares method and a procedure to determine the optimal averaging period for river inflow. Results from Charlotte Harbor indicate that, under average (70 m3 s−1) river inflow, 95% of the original water present in the harbor flushes into the gulf in 130 d.

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