Modern fluvial sediments provide important information about source-to-sink process and regional tectono-magmatic events in the source area, but many factors, e.g., chemical weathering, sedimentary cycles and source-rock types, can interfere with the establishment of the source-sink system. The Lalin River (LR) and the Jilin Songhua River (JSR) are two important tributaries of the Songhua River in the Songnen Plain in NE China. They have similar flow direction, topography and identical climate backgrounds, but have notably different parent-rock types in the headwater, which provides an opportunity to explore the influencing factors of river sediment composition. To this end, the point bar sediments in the two rivers were sampled for an analysis of geochemistry (including element and Sr-Nd isotopic ratios), heavy mineral and detrital zircon U-Pb dating. The results are indicative of the fact that the two rivers have the similar geochemical composition (e.g., elements and Sr isotopes) as well as chemical weathering (CIA = 51.41–57.60, CIW = 59.68–66.11, PIA = 51.95–60.23, WIP = 56.00–65.47, Rb/Sr = 0.38–0.42) and recycling (SiO2/Al2O3 = 5.79 and 5.03, ICV = 1.0 and 1.2, CIA/WIP = 0.81–1.03) characteristics, showing a major control of climate on the low-level weathering and recycling of the river sediments. However, there are significant differences in the detrital zircon U-Pb age (a significant Mesozoic age peak for the LR but an additional Precambrian peak for the JSR), Nd isotope ratio (−6.2812–8.5830 and −8.1149–10.2411 for the LR and the JSR, respectively) and to a certain extent heavy mineral composition (e.g., for the < 63 μm fraction, a dominance of hornblende and magnetite in the LR, but haematite-limonite in the JSR) in the two river sediments, indicating that source rocks largely control the composition of the river sediments. Some of the major tectono-magmatic events (e.g., crustal growth and cratonisation of the North China Craton, closure of the Paleo-Asian Ocean, subduction and rollback of the Paleo-Pacific plate) occurring in the eastern Songnen Plain are well documented in the JSR sediments but not in the LR, the difference of which is largely regulated by the source rocks in the source area.