River ecosystems are being degraded by various environmental factors across multi-spatial scales. In general, aquatic organism conservation aims to explore the relationship between aquatic organisms and environmental factors across multi-spatial scales, and to discern the scale at which the biological integrity of aquatic organisms is affected. We collected data about fishes and riparian habitat conditions at 15 sampling sites in the Taizi River basin during August, 2009. In parallel, we collected data on land use at the both of catchment and reach scales by interpreting the satellite images. We explored the relationship among the fish index of biotic integrity (F-IBI), land use at two scales, and riparian habitat condition. The results showed that riparian habitat condition is relatively better in the upper regions than the lower regions of rivers, due to a percentage increase in farmland and urban areas in the lower regions. F-IBI showed a positive correlation with the proportions of natural areas, but showed a negative correlation with the proportions of farmland and urban areas. F-IBI exhibited a stronger response to the proportion of farmland at the catchment scale, and to the proportion of urban areas at both scales. Compared to farmland, the same percentage increase in urban area resulted in a faster decrease of F-IBI. Substrate, water quality, and anthropogenic disturbances were three key riparian habitat parameters that significantly degraded F-IBI. These three parameters decreased with increasing proportions of farmland and urban areas. Farmland showed a significant effect on the three parameters at the catchment scale, whereas urban areas only significantly affected substrate and water quality at both scales.