This dataset includes species composition and abundances of macrobenthic faunal communities along three transects of Heraklion Bay (H2, H5, H7). The H2 transect is located in the wider marine area of the wastewater treatment plant of Heraklion city. Sampling was carried out during three different sampling surveys and periods — June 2010, June 2015, and August 2024 — at different depths (10, 20, 30, 40, 50, 100 and 200 m) along the soft-bottom continental shelf, as part of different research projects (MARBEFES, Marine Biology, Biotechnology & Aquaculture, monitoring program). A detailed comparison of species composition and abundance of macrobenthic faunal diversity among different depths and sampling periods is given, thus contributing to understanding the spatial and temporal trends and changes due to multiple environmental and human-induced stress.