River-ocean continuums are rich environments key to the transformations of organic matter and nutrients from many sources. Human impacts on these ecosystems can be local, upstream, or global. Particulate organic matter provides one tool for exploring these processes; inventories and carbon and nitrogen stable isotopes are useful indicators. This study conducted comprehensive field investigations from the upper reaches of the Yangtze River to the coastal waters to explore the distribution and spatial-temporal variation of particulate organic carbon (POC) and nitrogen (PON), and dissolved organic carbon (DOC) in surface waters from April–May (Spring) and October–November (Autumn) 2014. Carbon and nitrogen isotopes (δ¹³C and δ¹⁵N) were used to assess organic matter sources. Many environmental factors were also measured. PON and POC exhibited similar spatial-temporal variations along the river mainstream. POC increased from the upper to lower reaches, similarly in both seasons; POC declined seaward from the river mouth. In contrast, PON showed greater seasonal and spatial variations along the continuum, with greater primary production in offshore areas. DOC along the continuum was higher in autumn, likely related to greater river discharge and warmer waters. The DOC/POC ratios by weight were >1 in most samples except for the ones collected from the turbidity maximum zone, suggesting that DOC contributed to a larger fraction of the total organic matter inventories. End-member mixing models revealed that the proportion of organic matter from upstream (allochthonous) sources was >70% in the mainstream during both seasons. In coastal waters, the proportion of allochthonous sources was only >57%. Compared with other major world rivers, DOC and allochthonous POC are especially high in the Yangtze River-ocean continuum. Human activities causing variations in terrestrial inputs are likely an important driving factor. In addition, the contribution of soil erosion caused by urbanization to riverine organic carbon cannot be ignored.