Suspended sediments, or total suspended solids (TSS), are an important factor for oyster habitat. While high concentrations of suspended sediments can cause a reduction of oyster density, some level of suspended sediment is required to supply oysters with necessary nutrients. In this study, characteristics of TSS variations in response to sea level rise (SLR) at two oyster reefs in Apalachicola Bay are investigated by coupled estuarine hydrodynamic and sediment transport modeling. A storm event in 1993 and a year‐long period in 2010 under recent sea level conditions are selected as the baseline conditions. Scenarios of river flow and sediment loads under SLR and climate change are obtained by downscaled global climate modeling. Compared to the baseline conditions, simulations of TSS indicate that predicted SLR yields a substantial decrease in TSS near the two oyster reefs. However, TSS levels differed at the two study locations. TSS changes by SLR revealed minimal impact on oyster habitat at the Dry Bar site (to the west of the mouth of the Apalachicola River) but are projected to have a significant impact at the Cat Point site (to the east of the Apalachicola River). At Cat Point, because SLR causes the increase of salt water intrusion from the Gulf through a large tidal inlet (East Pass), maximum sediment concentration is near zero for 0.2‐m SLR and equal to zero for 0.5‐ and 1.2‐m SLR. Therefore, SLR may result in a substantial loss of nutrients from suspended sediment in the oyster reef at Cat Point.