Longitudinal patterns in species richness of fish assemblages have been examined, and many studies have showed positive relationships between species richness and stream size. Although the processes providing the patterns, i.e., fish community organization, have been focused, paucity of available data has constricted to understand the processes. Thus, we have assembled enough data in fish assemblages of the Kiso, Nagara, and Ibi Rivers, and examined the processes by focusing on longitudinal patterns in similarity, evenness, species nestedness, and turnover. In addition, we have also examined effects of fragmentation by weir on longitudinal patterns and processes in fish assemblages since many large dams are constructed in the Kiso River whereas large dams are less constructed in the Nagara River. In the Kiso, Nagara, and Ibi Rivers, fish assemblages exhibited longitudinal gradients in species richness, but fish assemblages in the Kiso River show large variations in the patterns, compared to those in the Nagara and Ibi Rivers. In the study, I will examine how fish assemblages is organized along stream size and demonstrate processes providing longitudinal patterns in species richness.