From November 2021 to October 2022, 12 monthly samplings were conducted at Luokou Station in the lower Yellow River (Huanghe River) to measure dissolved organic carbon (DOC), chromophoric dissolved organic matter (CDOM), fluorescent dissolved organic matter (FDOM), nutrients, as well as the proportion of POC, δ13
C and δ15
N values in suspended particulate matter (SPM) in the river water. The results indicate that water and sediment regulation (WSR) has become a key factor in controlling the pattern of annual changes in various biogenic elements in the lower yellow river, and determines the upper and lower limits of its annual variation range. During the early stage of WSR, the pulsed increase of river discharge caused the concentration of DOC, CDOM and humic-like components in FDOM, and δ13
C and δ15
N to their lowest values in a year, through water dilution, while the CDOM spectral slope (S275–295
) reached its highest value. In the late stage of WSR, the above parameters reached their annual extreme values in the opposite direction. In the past 20 years, under the influences of WSR, watershed ecological environment protection projects and climate change, the concentrations of nutrients and DOC in the lower Yellow River have shown significant downward trends, while the increase in the proportion of organic matter in SPM has also shown preliminary signs. The concentrations, compositions, properties, and output fluxes of biogenic elements in the lower Yellow River are undergoing complex and profound changes, which will directly affect the marine ecological environment of the Yellow River estuary. This study helps us further understand the response characteristics and feedback mechanisms of major river biogenic elements, as well as their potential impacts on adjacent marine ecosystems, in the context of human activities.