The major tributaries to Flaming Gorge Reservoir contribute an average of about 97 percent of the total streamflow and 82 percent of the total load of dissolved solids. The Green River is the largest tributary, and for the 1957-72 water years it contributed 81 percent of the total streamflow and 70 percent of the total load of dissolved solids. The principal constituents in the tributary streamflow are calcium and sulfate during periods of lowest flow and calcium and bicarbonate during periods of highest flow.

Flaming Gorge Dam was closed in November 1962, and the most significant load changes of chemical constituents due to the net effect of inflow, outflow, leaching, and chemical precipitation in the reservoir have been load changes of sulfate and bicarbonate. The average increase of dissolved load of sulfate in the reservoir for the 1969-72 water years was 110,000 tons (99,790 t) per year, which was 40,000 tons (36,287 t) per year less than for the 1963-66 water years. The average decrease of dissolved load of bicarbonate in the reservoir for 1969-72 was 40,000 tons (36,287 t) per year, which was the same as the decrease for 1963-66.

Anaerobic conditions were observed in the deep, uncirculated part of the reservoir near the dam during the 1971 and 1972 water years, and anaerobic or near-anaerobic conditions were observed near the confluence of the Blacks Fork and Green River during the summers of 1971 and 1972.

The water in Flaming Gorge Reservoir is in three distinct layers, and the upper two layers (the epilimnion and the metalimnion) mixed twice during each of the 1971-72 water years. The two circulation periods were in the spring and fall. The water in the deepest layer (the hypolimnion) did not mix with the waters of the upper zones because the density difference was too great and because the deep, narrow shape of the basin probably inhibits mixing.

The depletion of flow in the Green River downstream from Flaming Gorge Dam between closure of the dam and the end of the 1972 water year was 4,500,000 acre-feet (5,550.8 hm³). Of this total, water stored in the reservoir accounted for 3,500,000 acre-feet (4,317.2 hm³), evaporation consumed 700,000 acre-feet (863.4 hm³), and 300,000 acre-feet (370.0 hm³) went into bank storage.

The net load of dissolved solids added to the river system during the 1963-72 water years, due to leaching and chemical precipitation, was 1,730,000 tons (1,569,421 t). The leaching rate was 200,000 tons (181,436 t) per year for 1963-68,115,000 tons (104,326 t) per year for 1969-70 and 150,000 tons (136,077 t) per year for 1971-72. It appears that the leaching rates should decrease in the future since the reservoir level in 1972 was near maximum pool level.

The most significant increase in concentration of the chemical constituents in the water below the reservoir involved the sulfate ion, which increased from about 115 milligrams per litre (42 percent of the anions) in 1957 to about 200 milligrams per litre (54 percent), in 1972. But the highest concentration, about 290 milligrams per litre (58 percent), occurred in 1963, immediately after closure of the dam.

Prior to closure of the dam, the average monthly temperature of the Green River below the damsite ranged from 0°C to 19.5°C as compared to 3.5°C to 10.0°C after closure.