AbstractIn the northern Gulf of Mexico shelf, the Mississippi‐Atchafalaya River System (MARS) impacts the carbonate system by delivering freshwater with a distinct seasonal pattern in both total alkalinity (Alk) and dissolved inorganic carbon (DIC), and promoting biologically driven changes in DIC through nutrient inputs. However, how and to what degree these processes modulate the interannual variability in calcium carbonate solubility have been poorly documented. Here, we use an ocean‐biogeochemical model to investigate the impact of MARS's discharge and chemistry on interannual anomalies of aragonite saturation state (Ω_Ar). Based on model results, we show that the enhanced mixing of riverine waters with a low buffer capacity (low Alk‐to‐DIC ratio) during high‐discharge winters promotes a significant Ω_Ar decline over the inner‐shelf. We also show that increased nutrient runoff and vertical stratification during high‐discharge summers promotes strong negative anomalies in bottom Ω_Ar, and less intense but significant positive anomalies in surface Ω_Ar. Therefore, increased MARS discharge promotes an increased frequency of suboptimal Ω_Ar levels for nearshore coastal calcifying species. Additional sensitivity experiments further show that reductions in the Alk‐to‐DIC ratio and nitrate concentration from the MARS significantly modify the simulated interannual Ω_Ar patterns, weakening the positive surface Ω_Ar anomalies during high‐discharge summers or even producing negative surface Ω_Ar anomalies. Our findings suggest that riverine water carbonate chemistry is a main driver of interannual variability in Ω_Ar over river dominated ocean margins.