Fertilization can cause obvious shifts in nitrate-reducing community composition in agricultural ecosystems; however, little is known about the behaviors and functional characters of isolated nitrate reducers adapted to a specific environment. In this study, 849 nitrate-reducing bacteria were isolated from various fertilization treatments in a long-term paddy field experiment; the isolates were further characterized in functions with both culture-dependent and independent methodologies. The results showed that CK (no fertilizer) treatment had four genera with even relative abundance, whereas the other three treatments had their own predominant genera with Chromobacterium in nitrogen (N) fertilizer, Serratia in NPK (nitrogen, phosphorus, and potassium fertilizer) and Enterobacter in NPKC treatment (NPK plus rice straw). The isolates of Serratia and Enterobacter grew faster and produced significantly more nitrites than those of Chromobacterium and Burkholderia in the normal growth medium, suggesting that the dominant isolates from nutrient-rich environment, such as NPK and NPKC treatments, are better adapted to high nutritional conditions. On the contrary, the strains of Chromobacterium and Burkholderia possessed stronger nitrite production ability in comparison with the isolates of Serratia and Enterobacter in the diluted growth medium, indicating that the selected isolates from CK and N treatments have the capability to develop under nutrient-limiting conditions. Our results indicated that the behaviors and functions of nitrate reducers appears to be important in adapting to their dwelling habitats.