In order to assess how the last sea level rise affected the Aegean archipelago, we quantified the magnitude and rate of geographic change for the Aegean islands during the last sea-level-rise episode (21 kyr BP–present) with a spatially explicit geophysical model. An island-specific Area-Distance-Change (ADC) typology was constructed, with higher ADC values representing a higher degree of change. The highest fragmentation rates of the Aegean archipelago occurred in tandem with the largest rates of sea-level-rise occurring between 17 kyr and 7 kyr ago. Sea-level rise resulted in an area loss for the Aegean archipelago of approximately 70%. Spatiotemporal differences in sea-level changes across the Aegean Sea and irregular bathymetry produced a variety of island surface-area loss responses, with area losses ranging from 20% to > 90% per island. In addition, sea-level rise led to increased island isolation, increasing distances of islands to continents to > 200% for some islands. We discuss how rates of area contractions and distance increases may have affected biotas, their evolutionary history and genetics. Five testable hypotheses are proposed to guide future research. We hypothesize that islands with higher ADC-values will exhibit higher degrees of community hyper-saturation, more local extinctions, larger genetic bottlenecks, higher genetic diversity within species pools, more endemics and shared species on continental fragments and higher z-values of the power-law species-area relationship. The developed typology and the quantified geographic response to sea-level rise of continental islands, as in the Aegean Sea, present an ideal research framework to test biogeographic and evolutionary hypotheses assessing the role of rates of area and distance change affecting biota.