Above average precipitation and runoff between 1980 and 1985 have raised the water-surface elevation of Harney, Mud, and Malheur Lakes in eastern Oregon to the highest levels recorded and have caused mixing and interflow of water among the three lakes. A 50% increase in specific conductance throughout Malheur Lake from 1984 to 1985 resulted from an increase in sodium and chloride concentrations, probably caused by the flow of saline water from Harvey Lake and dissolution of evaporites in flooded areas around it. Arsenic and boron concentrations increased during the two years. Algal productivity was highest towards the center of Malheur Lake. Concentrations of major ions in the Malheur River during the 1985 irrigation season were dilute in upstream reaches because of flow releases from reservoirs; increasing in a downstream direction because of irrigation-return flow. Concentrations also increased with time during irrigation season, with the highest concentrations occurring in October after most diversions for irrigation were discontinued. Mass-balance equations were used to simulate mixing of Malheur Lake with Malheur River water to estimate the water quality that would occur at different points along Malheur River. Simulations of sodium and chloride concentrations and specific conductance values based on August river-flows during irrigation season, show a gradual increase from the headwaters downstream to Hope and greater increases downstream of Hope. After irrigation ceases, the simulated water quality becomes uniform throughout the river, because proposed lake flows are then the principal source of Malheur River flows. Arsenic and boron concentrations increase much more than expected between Namorf and Little Valley; thermal springs could be the source of arsenic and boron in this reach. Groundwater coming in contact with arsenic rich soils may also contribute to the elevated arsenic levels found in the river. At the end of the irrigation season, arsenic concentrations were measured at 85 microg/L in this 12-14 mi reach. Increasing inflows from Malheur Lake Should reduce arsenic levels between Namorf and the mouth, especially after irrigation ceases.