Abbotts Lagoon is part of Point Reyes National Seashore, located about 40 miles northwest of San Francisco and about 20 miles south of Bodega Bay. Water-quality samples were collected quarterly during water year 1999 at a site in each of three connected lagoons that make up Abbotts Lagoon and at a site in its most significant tributary. The quarterly samples were analyzed for major ions, nutrients, and chlorophyll-a. A bed-sediment sample was collected in each lagoon during August 1999 and was analyzed for organic carbon, iron, and total phosphorus. Seven tributaries were sampled during a February 1999 storm and four during an April 1999 storm. These samples were analyzed only for nutrients. One storm sample collected in April 1999 from a tributary downstream of the I Ranch dairy was analyzed for a suite of 47 compounds indicative of wastewater. Continuous water-level recorders were installed in the most significant tributary and the two largest lagoons for portions of the study. A water budget analysis for an April 2000 storm indicated that the main tributary accounted for 85 percent of surface inflows to Abbotts Lagoon. The portion of the surface inflow from the main tributary was lower in the February 1999 storms and is a function of upstream storage and vegetative growth in the tributary basins. Another water budget analysis for a period of no surface inflow (June and July 2000) indicated that the net ground-water contribution was an outflow (seepage) from Abbotts Lagoon of about 0.3 ft3/s. Salinity increased and nutrient concentrations decreased from upstream to downstream in the chain of lagoons. The lower lagoon, nearest the ocean, had less organic carbon and total phosphorus in the bed sediment than the upper lagoons. The two tributaries originating in the I Ranch dairy had the highest concentrations of nutrients in storm runoff, and the highest loading rates and yields of ammonia and phosphorus. These tributaries account for only 10.3 percent of the area drained by the sampled tributaries, but contributed 83 percent of the ammonia load and 79 percent of the orthophosphate load. The basins with the highest nutrient loading rates and yields had the highest percentage of dairy and (or) ranching impacted land use and, to a lesser extent, grazing land use. The ratios of inorganic nitrogen to phosphorus in the lagoons ranged from 0.1 to 9.5 in the upper lagoon, 0.10 to 0.15 in the middle lagoon, and 0.05 to 0.10 in the lower lagoon. Thus, there is an abundance of phosphorus in the lagoons, and nitrogen appears to be limiting the growth of phytoplankton. Two sterols indicative of fecal material were among 11 compounds detected in the sample collected for analysis of wastewater indicators from a tributary downstream of the I Ranch dairy.