Small-to-medium sized rivers play an important role in aquatic ecosystem functioning. In developing countries, limited by the number of monitoring sites in small-to-medium sized rivers, a single standard river health assessment method may not be able to reflect the actual situations under the pressure of increasing human activities and water conservancy projects. How to assess the health status of these rivers is of global concern. In this study, a small-to-medium sized river in China - Qiaobian River (QBR) was assessed by two essential river health assessment methods, i.e., Macroinvertebrate habitat suitable curve (M−HSC) and Pressure-State-Response framework (PSR). The applicability of the two methods was evaluated. The results demonstrated that both methods were suitable and achieved a better accuracy than water quality assessment framework, a standard method that has been widely applied to small-to-medium sized rivers in China, while minor differences in effectiveness were found between the two methods. Although both PSR and M−HSC methods showed the same health degree in wet season, M−HSC is more recommendable due to its convenience. On the contrary, in dry season, PSR better reflected the actual situations of QBR than M−HSC. The PSR was more applicable to urban rivers when evaluating the impacts of anthropogenic disturbances to river health, in contrast to M−HSC which was better suitable for rivers in rural areas to evaluate the effects of water conservancy projects. Our findings provide a new perspective on assessing health of small-to-medium sized rivers and important implications for ecological indication and conservation.