In 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 (ΩAr). 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 ΩAr 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 ΩAr, and less intense but significant positive anomalies in surface ΩAr. Therefore, increased MARS discharge promotes an increased frequency of suboptimal ΩAr 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 ΩAr spatial patterns, weakening the positive surface ΩAr anomalies during high-discharge summers or even producing negative surface ΩAr anomalies. Our findings suggest that riverine water carbonate chemistry is a main driver of interannual variability in ΩAr over river dominated ocean margins.