Spatial, temporal, and environmental trends of fish assemblages of the UMRS Barko, V. A., B. S. Ickes, D. P. Herzog, R. A. Hrabik, J. H. Chick, and M. A. Pegg. 2005. Spatial, temporal, and environmental trends of fish assemblages within six reaches of the Upper Mississippi River System. U.S. Geological Survey, Upper Midwest Environmental Sciences Center, La Crosse, Wisconsin, February 2005. Technical Report LTRMP 2005-T002. 27 pp. ABSTRACT We investigated differences in adult and young-of-the-year (YOY) fishes within each of the six Long Term Resource Monitoring Program study areas, using monitoring data from 1993 to 2001. Our objective was to investigate the relative roles of seasonal, annual, in situ, and physical habitat factors in explaining assemblage structure patterns within the Long Term Resource Monitoring Program study areas. Adult and YOY assemblage structure within each reach was dominated by one to three numerically abundant species. The percent of the total abundance for which these species accounted was 10 88% and varied among age classes and study areas. Physical habitat classes were only weakly associated with differences in fish assemblage patterns within each study area. The amount of variation in fish abundance explained by physical habitats varied among the reaches. Differences among physical habitat classes accounted for 3 23% of the variation in the adult fish assemblage and for 3 20% of the difference in the YOY fish assemblage within each reach of our study area. Factors associated with interannual differences in environmental conditions were strongly correlated to patterns in assemblage structure within each of the six study areas. This was particularly true for YOY assemblages. Such a result would not have been attainable without long-term standardized data. Little is known regarding YOY assemblage patterns and dynamics in large river systems and long-term data sets are vital for continued investigation. The influence of environmental gradients on fish assemblage structure varied among the six study areas and explained 9 31% of the variation in assemblage structure. In the northern four reaches, water velocity was one of the primary factors associated with differences in fish assemblage structure. In the Unimpounded Reach (Upper Mississippi River) and Illinois River study areas, river elevation was one of the primary factors associated with differences in assemblage structure. Depth of gear deployment was influential in explaining differences in assemblage structure patterns in all reaches except the Upper Mississippi River Pool 4 and the Illinois River study areas. In all study areas, the amount of variation in fish abundance patterns explained by sampling period was relatively low. However, assemblage structure differed among sampling periods. In the northern reaches, sampling periods 2 and 3 were the most similar. KEYWORDS fishes, Illinois River, impounded, long-term, LTRMP, Mississippi River, ordination, unimpounded, YOY