As a response to climate change and sea-level rise, new nourishment strategies for low-lying sandy coasts are developed. These interventions affect the habitat quality of coastal ecosystems for benthic communities. Unraveling the relationship between benthic fauna and their environment facilitates the design of sustainable management strategies for the coastal ecosystem. At the ebb-tidal delta of Ameland, The Netherlands, a unique dataset of 166 benthic and sediment samples is collected and allowed for an investigation of the macrobenthic fauna distribution at the spatial scale of morphological features. The benthic community at the ebb tidal delta is composed of species capable of withstanding the dynamic nature of these sandy coastal ecosystems. Despite the dynamic environment, the geomorphology of the ebb-tidal delta is reflected in the benthic species distribution. Distinct species assemblages were identified, covering a gradient of physical stress from extremely exposed to waves or currents, to relatively low energetic environments such as found on the delta plane seaward of the ebb-tidal delta terminal lobe. This gradient is reflected in the median grain size, organic matter content, and oxygenation of the sediment. A second gradient distinguishes well-sorted, mainly wave-exposed sediments from less well-sorted, mainly current-exposed sites. The functional characteristics of the benthic fauna show a clear contrast between the three most exposed, and the three most sheltered assemblages. Small, short-lived, surface deposit-feeding, highly mobile, burrowing organisms dominate in the most exposed sites, whereas with increasing shelter also larger, long-lived, filter-feeding and sessile organisms become more dominant. The functional characteristics suggest that the fauna of the most exposed sites will likely show a fast recovery of disturbance by sand nourishments. A much longer-lasting effect can be expected on sheltered parts of the ebb-tidal delta.