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Ecosystem functions of rivers have been greatly impaired due to the negative effects of human actions on river structures in different regions of the Earth during the last decades. It is an urgent task to understand the complete structures and ecosystem functions of a natural rive for restoration of the impaired river ecosystems. A natural river is composed of the repeatedly occurring rapid-pool-benchland system, i.e., a basic structural unit. We respectively selected three of the rapid-pool-benchland systems in the upper, middle and lower reaches of the Duliu River, a natural river in China as materials and tested the abundance of microorganisms in the sediments of these systems with plate counting method and a MPN (most-probable-number) method and the activity of enzymes with titration or colorimetric methods. Results indicated that the number of bacteria was far more than ammonifiers, actinomycetes, fungus and denitrifying bacteria in the sediments of all these rapid-pool-benchland systems. In each of the rapid-pool-benchland systems, all the microbial abundance in the sediments of the pools was always highest, and that of the rapids was lowest. In the upper reach, the microbial abundance was more than the middle and lower reaches. Catalase activity in the sediments of the benchlands was higher than the rapids and pools but phosphatase activity in the pools was higher than the rapids and benchlands. Phosphatas and urease activities were significantly correlated to the abundance of the bacteria, ammonifiers, actinomycetes, fungus and denitrifying bacteria in the sediments. The rapid-pool-benchland systems in a river obviously affect the microbial abundance and catalase and phosphatase activities related to biochemical functions in the sediments. However, the microbial abundance only indicated a middle-level correlations (r ranges from 0.434 to 0.836, p<0.05) with the activity of four extracellular enzymes. The study clarifies if the repeatedly occurring rapid-pool-benchland systems, a kind of habitat heterogeneity in a river have an effect on the microbial abundance and enzyme activity in the sediments, and further the relationships between the microbial abundance and enzyme activity.