San Juan River Recovery Implementation Program Summary Report 1991-97

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run habitat within the study area was similar during low and high flows. Run habitat was generally reduced in canyon reaches (RM 0 to RM 67) except below RM 20. Shoal habitat was the second most abundant habitat type based on total surface area and ranged from 2.6 percent of the TWA during December 1992 to 7.3 percent during October 1993. Shoal habitat included sand and cobble shoals, and was most abundant between RM 80 and RM 110. Riffle habitat exhibited variability and appeared to be related to flow. Density (area/mile) of riffles was similar at high (June) and low (October) flow periods, averaging less than 10,000 square meters (m) per mile. However, at intermediate flows during December 1992 and July 1993, density of riffle habitat increased to above 10,000 m per mile. Highest densities of this habitat were found in canyon reaches (RM 0 to RM 67) during this period. In 1994, however, mapping of new areas higher in the system revealed two major riffle areas between RM 160 to RM 180 and RM 210 to RM 224 (Bliesner and Lamarra 1995). It was speculated that the primary and secondary production from these areas may represent an important energy source for the native fish community. Slackwater and low velocity habitats represented only a small percentage of the total habitat available. Slackwater habitats composed 0.2 to 1.2 percent of the TWA during the periods mapped, with the highest percentage occurring during low flow in October 1993. Low velocity habitats comprised 1.3 to 1.9 percent of the habitat available between RM 82 to RM 158 with the highest relative availability during both July and October 1993. Within a larger reach, between RM 2 and RM 158, low velocity habitat composed 2.1 percent of the TWA during July 1993. The density of vegetative associated habitats was strongly related to flow, with the highest density occurring during peak flow in June 1993. The dramatic increase in this habitat type during this period was due to inundation of vegetated shoreline areas at flows of 7,200 to 9,960 cfs. These flows were sufficient to inundate large quantities of riparian vegetation, submerged islands; and rewetted abandoned channels that had been revegetated. Mapping at lower flows during December 1993, July 1993, and October 1993 showed that densities of vegetative associated habitats were relatively low. Shannon - Wiener diversity indices indicated that habitat was most diverse during low flow periods in December 1992 (Index = 1.42) and October 1993 (Index = 1.42). Habitat diversity was lowest (Index = 0.763) during peak flows in June 1993 and increased to 0.918 during lower flows in July 1993. Analysis of aerial videography and habitat mapping conducted during 1994 (Bliesner and Lamarra 1995) produced similar results as seen in 1993. Runs were the most abundant habitat type during both high and low flow periods. Vegetative associated habitats was highest during peak flows in June and decreased substantially by August. Relative abundance of riffle, shoal, low velocity, and slackwater habitats was higher during August than in June. Analysis of aerial videography and habitat mapping conducted in November 1994 and April and September of 1995 from RM 2 to RM 180 showed generally similar trends to those of previous years. One exception appeared to be in the vegetative associated habitats, which increased during higher flows in 1994 but appeared to show the opposite trend in 1995. Another difference was the substantial drop in the percentage of TWA represented by low velocity habitat in September 1995 (1.9 percent) compared to August 1994 (4.6 percent). This difference may have been related to San Juan River Recovery Implementation Program December 1997 Summary Report 15 PR -602 -1