Dam construction profoundly alters sediment organic matter regimes in large rivers. Yet, the underlying mechanisms and how cascade reservoirs jointly shape organic matter sources remain insufficiently understood. Here, we quantified organic matter sources across five cascade reservoirs in the middle–lower Lancang River using stable isotopes with a Bayesian mixing model. We found that algal-derived organic matter dominated during the dry season and in reservoirs with longer retention, whereas terrestrial organic matter prevailed during the wet season and intensified downstream with increasing watershed inputs. The structural equation model analyses demonstrated that reservoir regulation and seasonality influenced organic matter sources indirectly through nutrient dynamics rather than through direct hydrological forcing. Hydrodynamic conditions, represented by a composite index derived from hydraulic retention time and backwater length, were positively associated with nutrient enrichment in both water and sediments, whereas temperature showed a negative relationship with sediment nutrients; these nutrient variations were further linked to increased contributions of terrestrial, algal, and sewage-derived organic matter. Complementary boosted regression tree analyses further identified the key environmental predictors shaping organic matter partitioning. Water temperature together with sediment nutrients formed the core controls on the balance between terrestrial and algal organic matter (><span> </span>48<span> </span>% cumulative influence). Hydrodynamic factors were crucial for sewage-derived organic matter, with water depth and retention time jointly contributing 35.2<span> </span>% of its variability. Together, these results reveal that organic matter provenance in cascade systems emerges from the coupled effects of reservoir-induced nutrient regulation and temperature–hydrology interactions, producing source dynamics distinct from single-reservoir systems. This study provides mechanistic insights needed to improve reservoir ecosystem management and underscores the importance of integrating cascade-scale nutrient regulation into future assessments of human impacts on riverine carbon cycling.