Organic matters with a variety of the origins are discharged into river ecosystems from the watersheds. These organic matters sustain riverine food webs by being decomposed and incorporated through microbes and benthic invertebrate. However, although fungi are an important component of microbes, little is known on how fungal communities are shaped and thus change along river gradients. Since it is likely that amount and number of different organic matters increase toward downstream, we hypothesized that α-diversity of fungal species also increase along river gradients. Indeed, this hypothesis was supported when we analyzed fungal communities grown on cobble surface at various sites of the Natori River (Sendai, Japan) in fall, 2011. In this study, the same analysis was done with samples collected in spring, 2012, at the same river system to examine generality of the hypothesis. Compared with the results in fall, spatial changes in fungal species diversity along the riverine were not remarkable in spring, suggesting that factors shaping fungal communities differed between the seasons. Based on these results with data of water chemistry and land use and land cover in the watershed, we will ague crucial factors causing temporal and spatial variations of riverine fungal communities.