Headland and groyne sand bypassing greatly influences embayment dynamics at medium to long timescales, but is often disregarded or partially included in reduced-complexity shoreline models. This study explores how accounting for subaqueous sediment bypassing in a shoreline model affects mean embayed beach planshape and spatial variability. We implement a generic parametrization of sand bypassing in the LX-Shore model, with simulations on a synthetic embayment in two configurations: "full bypassing" (FB) where the sediments bypass the obstacle in the surfzone and beyond, and "shoreline bypassing" (SB) where bypassing occurs only when the shoreline extends beyond the obstacle. Time-invariant wave simulations show significant differences in updrift shoreline position between FB and SB. Simulations with time-varying wave angles and fixed wave height and period reveal that FB significantly impacts the embayment mean planform and spatial variability: FB reduces beach rotation by about 1/3, particularly under slightly oblique and slightly asymmetrical wave climates, and decreases shoreline curvature, especially under highly oblique wave climates. Downdrift shoreline erosion may be overestimated by up to 20% under SB. Our simulations provide new insight into the influence of subaqueous sand bypassing on embayed beach dynamics and emphasize the importance of including this process when modelling shoreline evolution in coastal embayments.