Algae are sensitive to the changes of water environment. The species composition and individual quantity of algae are closely related to the living environments and change with environmental variation. Therefore, algae are usually used as an indicator to assess river health. Aquatic algae can be divided into periphytic algae and phytoplankton according to their inhabiting behaviors. In previous studies, some researchers applied phytoplankton in river health assessment, but some other researchers applied periphytic algae in river health assessment. However, as regards which of periphytic algae and phytoplankton is more suitable in river health assessment, or whether no significant difference exists in the suitability of periphytic algae and phytoplankton in river health assessment, very few studies have been reported so far. In this study, taking Jialing River and Wujiang River as the subject, 11 sections in total were set in these two rivers, and the physi-chemical characteristics of water environment and the periphytic algal and phytoplankton communities at 11 sections were investigated in September, 2015. By using periphytic algal index of biological integrity (Pe-IBI) and phytoplankton index of biological integrity (Ph-IBI), together with comprehensive pollution index (CPI), the health status of Jialing River and Wujiang River were assessed. It was shown in this study that seven core parameters including total algal taxa number, Cyanophyta taxa number, Chlorophyta taxa number, individual proportion of Nitzschia, individual proportion of dominant taxa, Shannon-Wiener's diversity index, and evenness index, could be screened when the Pe-IBI was applied in the health assessment of Jialing River and Wujiang River. The negative correlations of Pe-IBI to CPI, total nitrogen content, and lead content of river water were found, which means that the biological integrity of periphytic algae decreased with the deterioration of water environment. However, when the Ph-IBI was applied in the health assessment of Jialing River and Wujiang River, only one core parameter (algae density) could be screened. Moreover, no correlation of Ph-IBI to comprehensive pollution index or to any of twelve water environmental factors was found. Our study revealed that, for rivers, periphytic algae is better than phytoplankton to indicate the water environmental quality, and consequently, periphytic algae is more suitable than phytoplankton to be used in river health assessment.