Due to anthropogenic activities within watersheds and riparian areas, stream water quality and ecological communities have been significantly affected by degradation of watershed and stream environments. One critical indicator of anthropogenic activities within watersheds and riparian areas is forest fragmentation, which has been directly linked to poor water quality and ecosystem health in streams. However, the true nature of the relationship between forest fragmentation and stream ecosystem health has not been fully elucidated due to its complex underlying mechanism. The purpose of this study was to examine the relationships of riparian fragmented forest with biological indicators including diatoms, macroinvertebrates, and fish. In addition, we investigated variations in these relationships over multiple riparian scales. Fragmentation metrics, including the number of forest patches (NP), proportion of riparian forest (PLAND), largest riparian forest patch ratio (LPI), and spatial proximity of riparian forest patches (DIVISION), were used to quantify the degree of fragmentation of riparian forests, and the trophic diatom index (TDI), benthic macroinvertebrates index (BMI), and fish assessment index (FAI) were used to represent the biological condition of diatoms, macroinvertebrates, and fish in streams. PLAND and LPI showed positive relationships with TDI, BMI, and FAI, whereas NP and DIVISION were negatively associated with biological indicators at multiple scales. Biological conditions in streams were clearly better when riparian forests were less fragmented. The relationships of NP and PLAND with biological indicators were stronger at a larger riparian scale, whereas relationships of LPI and DIVISION with biological indicators were weaker at a large scale. These results suggest that a much larger spatial range of riparian forests should be considered in forest management and restoration to enhance the biological condition of streams.