This dataset presents a sediment budget quantifying erosion in Neptune Pass and deposition in Quarantine Bay, both located on the lower east side of the Mississippi River in southeastern Louisiana, USA. The analysis is based on data collected in 2016 and 2022. The sediment budget was developed to assess sediment dynamics in this emerging distributary system, comparing scour in Neptune Pass to sediment accumulation in its receiving basin, Quarantine Bay. Erosional changes in Neptune Pass were quantified by differencing bathymetric data collected during a 2016 discharge survey with data from a 2022 multi-beam bathymetric survey. The spatial extent of the study area ranges from 29.500°N to 29.358°N latitude and from -89.525°W to -89.416°W longitude.