Increased algal blooms and loss of aquatic vegetation are critical environmental issues associated with shallow lakes worldwide. The increase in organic matter (OM) in both macrophyte-dominated areas (MDAs) and algae-dominated areas (ADAs) has exacerbated these problems. Most OM in water is concentrated as suspended particulate matter (SPM), which eventually migrates to the sediment. However, the detailed origins and fates of OM in water–SPM–sediment systems with coexisting MDAs and ADAs remain unclear. Therefore, in this study, we conducted monthly field investigations in Lake Taihu, focusing on OM-migration patterns in an MDA and an ADA. The C/N mass ratios, δ¹³C contents, and OM compositions of the water, SPM, and sediment were analyzed. Our findings revealed that autochthonous sources of OM prevailed in water, whereas terrestrial sources prevailed in SPM and sediment. Rapid decomposition processes of microbial- and algae-derived dissolved OM were discovered along the water–SPM–sediment pathways in both areas. A trend towards a shift from macrophytes to algae in the MDA was also discovered. Overall, the entire lake underwent a burial process of OM in both types of areas, with mineralization mostly occurring during the algal-bloom seasons and more strongly in the ADA. Furthermore, we deduced that a decrease in the OM-burial rate, but an increase in the mineralization rate, might occur after a complete shift from a macrophyte- to an algae-dominated status. Such a shift might change the carbon-cycle process in eutrophic shallow lakes and should be given more attention in future research.