The two-phase flow model SedFOAM was implemented along with an advection-diffusion solver to further understand temporal and spatial variability of scalar fluxes near a permeable rippled bed and their response to turbulent oscillatory flow conditions, sediment transport, and ripple migration. Numerical experiments were performed with scalars introduced by constant point sources at four different along-ripple locations. A time-dependent analysis of centroid location, spread, and area of the scalar plumes revealed distinct patterns for each injection point. Dye ejected from the left flank traveled the furthest, spreading up to $0.85\lambda$. The crest and right flank cases spread a total distance of $0.49\lambda$. The trough case exhibited the lowest spread of dye, with larger values near flow reversal likely due to vortex formation and ejection induced by pressure differences. Bulk statistics of turbulent scalar fluxes showed vertical fluxes dominating over horizontal fluxes, with maximum vertical-to-horizontal ratios of 1.6 on the right flank to 6.7 on the left flank. Flank cases exhibited the largest time-averaged normalized turbulent fluxes, with vertical values close to $1\times 10^{-3}$, which approximately doubles the $4.5\times 10^{-4}$ and $5.7\times 10^{-4}$ values of the crest and trough cases, respectively. These results highlight the role of flow characteristics and sediment dynamics in shaping scalar transport near the sediment-water interface.