The trace fossil Macaronichnus segregatis is interpreted to be produced by opheliid polychaetes that feed on epigranular microbes and organic matter commonly abundant in shallow-marine foreshore sands. Resulting traces are horizontal and typically random in orientation, but sometimes perpendicular to the shoreline. However, M. segregatis in Neogene sandy sediments from Santa Maria Island in the Azores shows a vertical or sub-vertical orientation. This is explained by vertical flow of pore waters and oxygenation fluctuations within the mixing zone between interstitial marine and freshwater aquifers–where epigranular microbes and organic matter are most enriched. On reefless volcanic oceanic islands like the Azores, insular shelves are invariably steep, narrow, and exposed to strong swell. Aquifers in this setting respond rapidly to small changes on account of limited shelf space and a high potential differential that stimulates a vertical shift in habitats. Freshwater aquifers on small, low-relief oceanic islands form a thin lens, the edges of which are wedged against marine interstitial waters and migrate up and down in response to changes caused by tides, storm surges and precipitation. During the Late Miocene–Early Pliocene, Santa Maria was an island fitting this description. Due to a waning volcanism, intense marine erosion and gradual submersion, the island developed a wide shallow platform covered by sandy shoals, as exemplified by the Malbusca section with vertical Macaronichnus. The process, however, is more acute on small, reflective beaches perched on rocky island coasts. Here, sand blankets cover small ramps cut in the basaltic bedrock, resulting in very limited freshwater aquifers subject to strong changes due to the low permeability of basalts. The mixing zone is therefore forced to migrate chiefly up and down, mostly due to tides. The same response is dramatic in sandy fillings trapped in basalt fissures. As a consequence, the producer of Macaronichnus was tightly constrained in movement. Both situations occur in the “Pedra-que-pica” section on Santa Maria.