There are large temporal and spatial variations of methane (CH4) emissions from natural wetlands. To understand temporal changes of CH4 production potential (MPP), soil samples were collected from a permanently inundated Carex lasiocarpa marsh and a summer inundated Calamagrostis angustifolia marsh over the period from June to October of 2011. MPP, dissolved organic carbon (DOC) concentration, abundance and community structure of methanogenic archaea were assessed. In the C. lasiocarpa marsh, DOC concentration, MPP and the methanogen population showed similar seasonal variations and maximal values in September. MPP and DOC in the C. angustifolia marsh exhibited seasonal variations and values peaked during August, while the methanogen population decreased with plant growth. Methanogen abundance correlated significantly (P = 0.02) with DOC only for the C. lasiocarpa marsh. During the sampling period, the dominant methanogens were the Methanosaetaceae and Zoige cluster I (ZC-I (TM)) in the C. angustifolia marsh, and Methanomicrobiales and ZC-I (TM) in the C. lasiocarpa marsh. MPP correlated significantly (P = 0.04) with DOC and methanogen population in the C. lasiocarpa marsh but only with DOC in the C. angustifolia marsh. Addition of C. lasiocarpa litter enhanced MPP more effectively than addition of C. angustifolia litter, indicating that temporal variation of substrates is controlled by litter deposition in the C. lasiocarpa marsh while living plant matter is more important in the C. angustifolia marsh. This study indicated that there was no apparent shift in the dominant types of methanogen during the growth season in the species-specific freshwater wetlands. Temporal variation of MPP is controlled by substrates and substrate-driven changes in the abundance of methanogenic archaea in the C. lasiocarpa marsh, while MPP depends only on substrate availability derived from root exudates or soil organic matter in the C. angustifolia marsh.