Both aquatic and terrestrial biodiversity information can be detected in riverine water environmental DNA (eDNA). However, the monitoring effectiveness (i.e., the proportion of aquatic and terrestrial biodiversity information detected in riverine water eDNA samples) is unknown. To investigate the monitoring effectiveness, we introduced the concept of watershed biological information flow (WBIF) and proposed that the monitoring effectiveness depended on the transportation effectiveness of the WBIF. Then, the monitoring effectiveness could be assessed in the WBIF framework. Here, we conducted a monitoring effectiveness assessment case study in a watershed on the Qinghai-Tibet Plateau according to analysis of the bacterial operational taxonomic unit (OTU) assemblages detected in riverine water eDNA samples and riparian soil eDNA samples during three seasons. The results showed that (1) the downstream-to-upstream monitoring effectiveness: only 76% of the bacterial OTUs could be detected 1 km downstream in spring and more than 97% and 96% could be detected in summer and autumn, respectively. (2) The river-to-land monitoring effectiveness: more than 62% of the bacterial OTUs in riparian soil eDNA samples could be detected in adjacent riverine water eDNA samples on rainy summer days and 16% and 48% could be detected on cloudy spring and autumn days, respectively. These results suggested that riverine water eDNA was viable for simultaneously monitoring aquatic and terrestrial bacterial biodiversity and that rainy days in summer or autumn were suitable sampling times on the Qinghai-Tibet Plateau. More studies on monitoring effectiveness in other taxonomies and in other watersheds with different climatic conditions are needed.