The collection, transport and transformation of sediments, nutrients, organic matter, energy and information are key topics in the studies on ecosystem processes. However, there is no systematic literature on watershed information flow (WIF) in watershed ecology. To promote research on the WIF, we proposed the concept of watershed biological information flow (WBIF) by referencing the concept of biological information flow, and defined it as the path, processes and control of biological information transport, exchange, interaction and feedback among different spaces and systems along with watershed ecosystem processes. We proposed that the key of WBIF research should focus on 1) the WBIF between land and river, branch and main stream, upstream and downstream and different patches, 2) the periodical fluctuation and trending drift of the WBIF, and 3) the impacts of geomorphologic, hydrologic situations and human activities on WBIF. We conducted a case study on the WBIF in the Shaliu River basin indicated by the environmental microbes in riverine water and riparian soil using environmental DNA technology. Shaliu River is one of the main inflowing rivers of Qinghai Lake, which has a relative simple watershed ecosystem. In the river, there is a simple aquatic ecosystem with low biodiversity and a migratory fish Gymnocypris przewalskii which migration between river and lake. On the land, there are dominant grassland and limited human activities. To reveal the essential features of WBIF driven by natural runoff, we compared the bacterial community (indicated by operational taxonomic units (OTUs)) from upstream riverine water samples with from downstream riverine water samples and from riverine water samples with from adjacent riparian soil samples. Results showed that (1) the WBIF from riparian soil to riverine water was driven by surface flow and subsurface flow and filtrated by environment change. Its transport efficiency was 62.76% in rainy day and 44.16% in sunny day. Correspondingly, their transport capacity was 68.49% and 56.82%, respectively; their environmental filtration was 8.38% and 22.38%, respectively. (2) The WBIF from upstream to downstream was driven by river flow and attenuated in transport. Its basic integrated transport efficiency was 97.41% per kilometer, in which the transport capacity was 99.42% per kilometer, the proportion of noneffective WBIF was 43.46%, and half-life distance of noneffective WBIF was 14.52 kilometers. (3) As the transport efficiency of the WBIF was mainly constrained by transport capacity of WBIF, precipitation drove the arising of surface flow, then enhanced the power of erosion and transportation, and finally promoted the increase of WBIF transport capacity and efficiency. (4) The WBIF increased the detectable biodiversity of sink aquatic ecosystem, but the increase of detectable biodiversity is limited rather than accumulated along the river.