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The Ruby Lake watershed (37°24'50"N, 118°46'15"W) is on the eastern slope of the Sierra Nevada in the John Muir Wilderness of the Inyo National Forest. Research in this basin began in 1986. The lake is the largest (12.6 ha) and deepest (maximum depth 35 m) of those we studied; it has the greatest volume (2 x 106 m3) and lies at the highest altitude (3,390 m). Ice typically covers the lake from November through May and continues into June and July during years with abundant snowfall. Ice thickness varied from 1 to 2 meters during the 8 years of record which corresponds to a displacement of 12-17% of the lake's volume. Ruby Lake is dimictic, turning over in the late spring and in the autumn. Strong to moderate thermal stratification occurred during both winter and summer. Maximum summer lake temperatures ranged from 11 to 16°C. Similar to Pear Lake, waters near the bottom of the lake rarely warm above 5°C, indicating that Ruby Lake probably does not mix completely during overturn. Associated with stratification were intervals of low hypolimnetic oxygen; however, unlike Pear Lake, no accumulation of hydrogen-ion, hydrogen sulfide, ammonium or iron was observed in Ruby.

Ruby Lake has the highest V/A index of the study catchments (0.47 m) indicating substantial lake influence on the quantity and quality of basin discharge. This influence was greatest in years such as 1992 when the quantity of runoff (0.44 meters) was insufficient to completely flush the lake. The lake outflow runs year-round, suggesting there is substantial groundwater and lake storage and release. Of the seven lake basins in the acid rain study, Ruby Lake has the largest catchment (gauged area 441 ha) and greatest watershed relief (812 m). The highest elevation in the catchment is 4,202 m asl and the basin has a northwestern exposure.

Bedrock in the Ruby Lake watershed is composed predominantly of 'quartz monzonite of the Mono recesses.' This rock is typically coarse-grained and strongly porphyritic, and contains minor amounts of hornblende and sphene. Bedrock outcrops, talus and boulders cover most of the catchment and soil cover is sparse; most soils are classified as Alpine Brown. The higher cirques of the basin contain talus fields and rock-covered glaciers. These glaciers are actively eroding the watershed, as evidenced by glacial flour in the major inflow to the lake. Two other significant runoff channels have been identified (1) the "Cirque Inflow" which drains a portion of the watershed southwest of the lake covered with bedrock, boulders and talus and (2) the "Mono Pass Inflow" which originates in the northern portion of the watershed containing large area of Alpine Brown soil and talus. Sparse stands of Whitebark and Lodgepole Pine are confined to areas along the north and northeast edge of the lake. Grasses, sedges and low shrubs are the dominant vegetation.