The correlation between dissolved barium (DBa) concentrations and those of silicon (DSi) in the modern ocean underpins the use of Ba as a palaeoceanographic proxy. However, the mechanisms behind their linkage and the exact processes controlling ocean Ba cycling remain enigmatic. We present the first combined measurements of stable Ba (δ¹³⁸Ba) and Si (δ³⁰Si) isotope compositions of seawater samples from the Congo River-dominated Southeast Atlantic margin. Together with Ba and Si fluxes, estimated based on ²²⁸Ra, we investigate the biogeochemical cycling of Ba and Si and their relationship during transport from the river mouth to the northern Angola Basin. In the surface waters, river-borne particle desorption/dissolution and shelf inputs (submarine groundwater discharge and/or porewater efflux) lead to non-conservative additions of both DBa and DSi to the Congo-shelf-zone. Compared to Si, the Ba flux shows more prominent amplification from the Congo River to the shelf zone, and the Ba addition is equivalent to 5.9 ± 4.9 % of the global freshwater Ba input. In the epipelagic and mesopelagic layers, Ba and Si are decoupled due to different depth intervals of barite precipitation and biogenic silica production. In the deep waters of the northern Angola Basin, we observe large enrichment of DBa, likely originating from high benthic inputs of the Congo submarine canyon and deep-sea fan sediments. Our results highlight a strong margin influence on marine Ba cycling and reveal fundamentally different mechanisms controlling the biogeochemical cycling of Ba and Si. The close association of DSi and DBa in the global ocean must therefore mainly be a consequence of the large-scale ocean circulation.