The circulation of water in Flaming Gorge Reservoir is caused chiefly by insolation, inflow-outflow relationships, and wind, which is significant due to the geographical location of the reservoir. During 1970-75, there was little annual variation in the thickness, dissolved oxygen, and specific conductance of the hypolimnion near Flaming Gorge Dam. Depletion of dissolved oxygen occurred simultaneously in the bottom waters of both tributary arms in the upstream part of the reservoir and was due to reservoir stratification. Anaerobic conditions in the bottom water during summer stratification eventually results in a metalimnetic oxygen minimum in the reservoir.

The depletion of flow in the river below Flaming Gorge Dam due to evaporation and bank storage in the reservoir for the 1963-75 period was 1,320 cubic hectometers, and the increase of dissolved-solids load in the river was 1,947,000 metric tons. The largest annual variations in dissolved-solids concentration in the river was about 600 milligrams per liter before closure of the dam and about 200 milligrams per liter after closure. The discharge weighted-average dissolved-solids concentration for the 5 years prior to closure was 386 milligrams per liter and 512 milligrams per liter after closure. The most significant changes in the individual dissolved-ion loads in the river during 1973-75 were the increase in sulfate (0.46 million metric tons), which was probably derived from the solution of gypsum, and the decrease in bicarbonate (0.39 million metric tons), which can be attributed to chemical precipitation.

The maximum range in temperature in the Green River below the reservoir prior to closure of the dam in 1962 was from 0°C in winter to 21°C in summer. After closure until 1970 the temperature ranged from 2° to 12°C, but since 1970 the range has been from 4° to 9°C.

The maximum range in temperature in the Green River below the reservoir prior to closure of the dam in 1962 was from 0°C in winter to 21°C in summer. After closure until 1970 the temperature ranged from 2° to 12°C, but since 1970 the range has been from 4° to 9°C.During September 1975, a massive algal bloom was observed in the upstream part of the reservoir. The bloom covered approximately 16 kilometers of the lower part of the Blacks Fork arm, 23 kilometers of the lower part of the Green River arm, and 15 kilometers of the main reservoir below the confluence of the two arms. By October 1975 the algal bloom had disappeared. Nutrient loading in the reservoir was not sufficient to maintain a rate of algal production that would be disastrous to the reservoir ecosystem. However, should the nutrient loading increase substantially, the quality of the reservoir water could probably deteriorate rapidly, and its use for recreation and water supply could be severely limited.