[Objectives] Compared to natural-formed tropical coral islands, newly-constructed coral islands exhibit distinct compactied clay layers due to the hydraulic filling and deposition during formation processes. To explore the hydraulic properties and hydrological conditions effects on rainfall infiltration, subsurface flow and coral sand transport. [Methods] This study focuses on the clay compaction layer in coral sand profiles. Through in-situ field investigations and sampling, we characterized the textural type and hydro-physical properties of coral sand at different depth. Laboratory rainfall simulation experiments were conducted to investigate hydrological responses and sand transport processes under varying profile compositions, comparing homogeneous slopes with those containing clay compaction layers. [Results] These results showed that coarse coral sand has a high hydraulic conductivity, whereas the clay compaction layer exhibits extremely low permeability. The saturated hydraulic conductivity of clay compaction layer was only 8% of the other coarse coral sand. The homogeneous slopes allowed complete rainwater infiltration without surface runoff generation, while clay compaction layers redirect 87% of rainfall as subsurface flow, triggering coral sand particle loss. Hydrological condition shifts from free drainage to saturated and seepage flows amplify the rates and total amount of subsurface runoff and sand transport, though the compaction layer with low-permeability may mitigates coral sand loss under seepage condition. [Conclusion] The clay compaction layer can significantly alter hydrological processes and sand transport, leading to shallow hydrological processes and the development of dissolution fissures. These findings have critical implications for improving our understanding of freshwater cycling processes and guiding eco-friendly engineering practices in coral islands.