A number of distinct shell middens have been recorded and excavated in Philippine cave sites. This paper attempts to understand the existence and composition of these shell midden deposits in caves by comparing them with palaeogeographic reconstructions of sea-level changes at the end of the Last Glacial Maximum up until the mid-Holocene. The palaeoshoreline reconstructions are created using existing bathymetric data and are processed in GRASS GIS software. Results show that the appearance and composition of shell midden deposits are directly related to changes in seascapes brought about by variations in sea level during the time period. Based on the Philippine dataset, it can be argued that the extensive exploitation of coastal resources most likely predates the appearance of these shell middens in present-day archaeological sites. The samples visible to the archaeologist at present are remnants of ever-changing island coasts and seascapes.