This dataset supports the results presented in the paper describing the IAP-SWBF framework for shallow-water bathymetry using ICESat-2 photon-counting LiDAR data. It includes representative ATL03 data segments, processed intermediate outputs, and the final results of underwater terrain photon extraction across a variety of aquatic environments. The dataset is organized to facilitate reproducibility of the proposed methodology and to support further comparison and evaluation of shallow-water bathymetric techniques. The associated code and additional resources are available at: https://github.com/lj-lijun/IAP-SWBF_Afterpulse_remove