The Zhe-Min mountainous rivers in SE China are characterized by stable tectonics, small–mesoscale drainage basins, relatively homogenous bedrocks, dense vegetation cover and high rainfall conditions. These rivers deliver loads of sediments and nutrients to the oceans and always indicate considerably high variability of sediment flux on short-term timescales. However, short-term sediment compositional variations and transport mechanism by these mountainous rivers remain poorly understood. Here we target the Minjiang River, use mineralogical and trace element geochemical data of suspended particulate matters (SPMs) within a one-year hydrological cycle (from October 2016 to October 2017), riverbed sediments (<0.063 mm fractions) and SPMs from the mainstream and major tributaries, to investigate their provenance and transport process. The results indicate that the SPMs in different seasons have strong seasonal geochemical heterogeneity, with highly positive correlations between several trace element ratios (e.g. La(CN)/Yb(CN) and Th/Sc) and runoff of the river. Riverbed sediments and SPMs collected in pairs have distinct geochemical compositions. The riverbed sediments have relatively low La(CN)/Yb(CN) (ca. 10–15) and Th/Sc (ca. 2–5) ratios, whereas the SPMs have La(CN)/Yb(CN) and Th/Sc ratio ranges of ca. 14–17 and ca. 4–7, respectively. These findings suggest a predominant hydrologic control on the Minjiang River sediment transport and geochemical compositions on a seasonal timescale. We conclude that exposed riverbed sediments are probably selectively recycled in dry-season sediment transport, whereas the flood-season SPMs are less mixed with riverbed sediments and are likely dominated by particulates directly from those tributaries and the upper mainstream. We favor that the Zhe-Min mountainous rivers are featured by rapid sediment delivery in response to hydroclimatic changes and have similar sediment transport behaviors with those small mountainous rivers in tectonically active regions of the subtropical East Asia (e.g. Taiwan). This case study also highlights the importance of multi-spatio-temporal scale, heterogeneous river input of chemical elements to the oceans.