In the shallow waters of the Bay of Concarneau (South Brittany, France), previous studies reported a dense settlement of the species Haploops (tube-dwelling bioengineer amphipod) that perfectly overlaps a field of pockmarks. A possible mechanistic link may therefore exist between the Haploops colonies and the shallow pockmarks. To test this hypothesis, interferometry sonar and sub-bottom profiler chirp data were acquired in two new areas located in the marine estuary of the Loire River, “La Lambarde” and “Le Croisic”. The new sites share the same sedimentary and geological characteristics as those found in the Bay of Concarneau. The three sites are similarly located in shallow and muddy environments above a faulted Middle Eocene formation that is incised by paleo-valleys. Despite different hydrodynamic conditions and estuarine influence, in the two new investigated areas, the Haploops also settle within the pockmarks field limits. To better constrain the association pockmarks/Haploops, we compared the sedimentary features, seismic signatures and total organic carbon (TOC) content of the sediment. Active pockmark chimneys displaying highly reworked profiles and slightly higher TOC contents suggest a local deeper source of organic matter, which might be an important source of nutrient for the Haploops. In Southern Brittany the pockmarks/Haploops spatial overlap is not a simple coincidence and may therefore present a general pattern for identification of settlement preferences of the specie.