Variations of strontium isotope ratios (87Sr/86Sr) in river systems are increasingly utilised to geochemically trace origin and movement patterns of migratory fish species. Accretionary calcified structures, such as otoliths, preserve 87Sr/86Sr signatures of the surrounding water during a fish’s lifetime. In this study, we present 87Sr/86Sr measurements of water samples and catfish otoliths collected in the estuaries of the Sine-Saloum (Senegal), the Gambia River (The Gambia), and the Volta River (Ghana) to assess their systematics and relationships with salinity. The three rivers possess distinct hydrological properties resulting in variable degrees of correlations between 87Sr/86Sr and salinity. The Gambia River (87Sr/86Sr of ~ 0.71209) proved exceptionally preconditioned for the approach due to well-defined geochemical end-members, allowing for quantitative estimates of salinity based on otolith 87Sr/86Sr measurements. The Volta River (~ 0.71392) presents a more complex case due the possible influence of multiple water sources to the main channel, while the inverse salinity gradient and excessive evaporation in the Sine-Saloum estuary (~0.70915) impede any significant correlations between 87Sr/86Sr and salinity. Bulk otolith 87Sr/86Sr values in the Gambia River and Volta River clearly depicted a mixed influence of seawater and riverine compositions, strongly encouraging the application of this approach for geochemical fingerprinting of critical NW African species.