Coral reef islands are among the most vulnerable landforms to climate change. However, our understanding of their morphodynamics at intermediate (seasonal to interannual) timescales remains poor, limiting our ability to forecast how they will evolve in the future. Here, we applied a semi-automated shoreline detection technique (CoastSat.islands) to 20 years of publicly available satellite imagery to investigate the evolution of a group of reef islands located in the eastern Indian Ocean. At interannual timescales, island changes were characterized by the cyclical re-organization of island shorelines in response to the variability in water levels and wave conditions. Interannual variability in forcing parameters was driven by El Niño Southern Oscillation (ENSO) cycles, causing prolonged changes to water levels and wave conditions that established new equilibrium island morphologies. Our results present a new opportunity to measure intermediate temporal scale changes in island morphology that can complement existing short-term (weekly to seasonal) and long-term (decadal) understanding of reef island evolution.