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~} C~) Ii-'" (D ~,. "', v., difference resulted from later spawning and habitat shifts, Many native species shift from using backwater nursery habitats to habitats with more current in late summer Of early fall, and those habitats were not sampled, Hence, the change in abundance may reflect this habitat shift. Lower numbers of nonnative species during higher runoff years may also result from later spawning by these species, rather than an actual lowering of the population, This information suggests that higher flows resulting from the reoperation of the Navajo Dam were not detrimental to channel catfish and common carp, but it is not clear how they affected nonnative cyprinids. The decline in nonnative species in the Green and Colorado rivers primarily involved nonnative cyprinids, Lack of seining in all habitats in the San Juan River primary channel during the 7-year research period precludes a complete analysis of nonnative cyprinid response riverwide. Hence, it is not clear if the declines in nonnative cyprinids seen in other rivers during higher spring runoff years also occurred in the San Juan River. There may be several reasons for this lack of expected response from nonnative species, Flows from Navajo Dam are limited to a maximum release of 5,000 cfs, so flows in the river below the mouth of the Animas River peaked at about 12,000 cfs during the 7-yearresearch period, Spring runoff during this period would have been higher without the dam, Some historic floods may have been more than 100,000 cfs (Bliesner and Lamarra 2000). Therefore, perhaps the magnitude of the flooding was not high enough to reduce numbers of nonnative species. Another potential reason for the stable or increasing populations of nonnative fishes is that the natural flow hypothesis may not fit all portions of the Colorado River system. Holden and Abate (1998) showed that red shiner numbers were not reduced in a portion of the Virgin River after large flood events, Whatever the reason, flow reoperation on the San Juan River did not consistently reduce nonnative species numbers, but as noted above, it improved habitat for native species. Holden (I 979) suggested that natural flow pattern and magnitude provided improved habitat and that native fishes appeared to be less affected by potential interactions with nonnative species in these situations, This appeared to be the case in the Green River, where nonnative fishes were abundant, but populations of Colorado pikeminnow were doing well (Bestgen et al. 1998, Trammell et al. 1999), !tis suspected that habitat for all life stages of Colorado pikeminnow is relatively optimal in the Green River and that this results in less impact from the nonnative fishes than it does in other rivers where the habitat is not as optimal. Recent studies of razorback sucker in the Green River suggest that as flooded bottomland habitat for larval and YOY fazorback sucker is restored, this species may also improve, even though nonnative fish numbers remain high (Modde 1996). If this hypothesis is correct, then improved habitat resulting from flow manipulation in the San Juan River will reduce the effect of nonnative fish interactions on native species, especially the two endangered species, without necessarily reducing nonnative fish numbers. September 2000 3-51 Program Evaluation Report