The present work aims to study the effects of waves on the transport and fate of sediments from submarine wastewater outfalls in relatively shallow waters. A hydrodynamic model both with and without wave effects was implemented, calibrated and validated for a case study in Baixada Santista, São Paulo state, Brazil. Suspended sediment discharges from five outfalls were included in both cases. To study the influence of wave conditions, three periods corresponding to mild, mean and strong waves were defined. The results from current-only and wave-current models were compared to identify differences in the transport and fate of outfall effluent sediments due to wave action. It was found that, if waves are not considered, the model simulates a continuous deposition process that results in unrealistic bed sediment accumulation. Significant wave-induced resuspension was observed in the vicinity of the outfall diffusers, even during mild wave conditions. Under mean and strong wave conditions, the affected sediment can be transported further by longshore currents and settle far away from the discharge location, reaching nearby coasts and channels. The observed events of resuspension are controlled by near-bed wave orbital motions that stir up bed sediments. Overall, results indicate that coupled wave-current models can help to better understand the fate of sediment-attached pollutants from outfalls and to identify areas of long-term environmental concern. In conclusion, it is suggested that future studies consider the potential effects of surface waves on the design and operational conditions of submarine sewage outfalls, especially for outfalls that discharge in relatively shallow waters.