Seasonal changes in water levels and flows in Big Cypress National Preserve (BICY) and Everglades National Park (EVER) affect water quality. As water levels and flows decline during the dry season, physical, geochemical and biological processes increase the breakdown of organic materials and the build-up of organic waste, nutrients, and other constituents in the remaining surface water. For example, concentrations of total phosphorus in the marsh are less than 0.01 milligram per liter (mg/L) during much of the year. Concentrations can rise briefly above this value during the dry season and occasionally exceed 0.1 mg/L under drought conditions. Long-term changes in water levels, flows, water management, and upstream land use also affect water quality in BICY and EVER, based on analysis of available data (1959-2000). During the 1980's and early 1990's, specific conductance and concentrations of chloride increased in the Taylor Slough and Shark River Slough. Chloride concentrations more than doubled from 1960 to 1990, primarily due to greater canal transport of high dissolved solids into the sloughs. Some apparent long-term trends in sulfate and total phosphorus were likely attributable, at least in part, to high percentages of less-than and zero values and to changes in reporting levels over the period of record. High values in nutrient concentrations were evident during dry periods of the 1980's and were attributable either to increased canal inflows of nutrient-rich water, increased nutrient releases from breakdown of organic bottom sediment, or increased build-up of nutrient waste from concentrations of aquatic biota and wildlife in remaining ponds. Long-term changes in water quality over the period of record are less pronounced in the western Everglades and the Big Cypress Swamp; however, short-term seasonal and drought-related changes are evident. Water quality varies spatially across the region because of natural variations in geology, hydrology, and vegetation and because of differences in water management and land use. Nutrient concentrations are relatively low in BICY and EVER compared with concentrations in parts of the northern Everglades that are near agricultural and urban lands. Concentrations of total phosphorus generally are higher in BICY (median values, 1991-2000, were mostly greater than 0.015 mg/L) than in EVER (median values, 1991-2000, less than 0.01 mg/L), probably because of higher phosphorus in natural sources such as shallow soils, rocks, and ground water in the Big Cypress region than in the Everglades region. Conversely, concentrations of chloride and sulfate are higher in EVER (median values in Shark River Slough, 1991-2000, mostly greater than 2 mg/L sulfate and 50 mg/L chloride) than in BICY (median values, 1991-2000, less than 1 mg/L sulfate and at most sites less than 20 mg/L chloride), probably because of the canal transport system, which conveys more water from an agricultural source into EVER than into BICY. Trace elements and contaminants such as pesticides and other toxic organic compounds are in relatively low concentrations in BICY and EVER compared with concentrations in parts of the northern Everglades near agricultural and urban sources. Concentrations rarely exceeded aquatic life criteria in BICY and EVER. Atrazine was the only pesticide found in water that exceeded the criteria (in 2 out of 304 samples). The pesticides heptachlor expoxide, lindane, and p,p?-DDE exceeded criteria in canal bed sediments in 1, 2, and 16 percent of the samples, respectively.