DNA microarray mounted 85 functional gene sequences related to carbon, nitrogen and sulphur cycles, chemical degradation, metal metabolisms, and energy flows was developed to evaluate the function and status of the environment. Total of 24 river water samples from 6 sampling stations in 2 rivers in 4 seasons were analyzed using constructed DNA microarray. The numbers and constitution of the functional genes were much affected by the seasonal change. Some of the functional genes related to methane oxidation, nitrite reduction, nitrogen fixation, aromatic compounds degradation (catechol 2,3-dioxygenase), alkane degradation (group I and III) and iron reduction were detected in most of all the samples, suggesting that these could be the general functions of the river environment. Some other functional genes related to ammonium oxidation, aromatic compounds degradation (catechol 1,2-dioxygenase) and alkane degradation (group II) can be a certain indicator for the evaluation of the environmental condition.