River ecosystems have been disturbed and aggravated by increasing human activities including those activities wherein forest area is changed to agricultural area in riparian zones and intensive fertilizer usage in agriculture. These anthropogenic activities lead to an increase in the light received by the surface of the river and nutrient (nitrogen and phosphorus) enrichment in the river. Denitrification driven by microorganisms in sediments is the most important path for the removal of nitrogen from aquatic ecosystems. The alteration of light intensity influences the denitrification process owing to the change in the amount of available organic carbon produced via the metabolism of algae and photosynthetic bacteria. We added slow-releasing fertilizer into the river to simulate nutrient enrichment similar to the effect of fertilization from the agricultural industry. We also covered a part of the stream surface to achieve conditions similar to those of rivers in headwaters with thick forest coverage. We selected six streams to conduct manipulated experiments at the core area in the natural reserve in the upper Jinshui River, Hanjiang, to assess the responses of denitrification to the different treatments-nutrient addition and coverage. We also analyzed subsequent changes in community structure and diversity of bacteria using the encoding nirS gene by MiSeq high-throughput sequencing technology. The results showed that artificial shading above streams can reduce the denitrification activity of sediments, relative abundances of dominant bacteria (Dechloromonas) and the diversity of bacteria as indicated by the encoding nirS gene. Furthermore, nutrient addition into the stream increased the denitrification activity of sediments, whereas there was a decrease in relative abundance of dominant bacteria and the diversity of bacteria. The preliminary results confirmed the increase in denitrification activity of stream sediments as a result of increasing light intensity and nutrient content. This study has allowed us to understand the denitrifying capacity of rivers and provides scientific primary data for river management.