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Summarization: Submarine groundwater discharge (SGD) contributes to the physical and chemical characters of coastal waters by discharging nutrients and contaminants, significantly impacting regional marine ecosystems and contributing to ocean chemical budgets. However, such groundwater discharge varies dramatically across scales and is often not comparable due to different model assumptions and field designs. We used a hydrologic model with integration of fundamental surface and subsurface processes to simulate the coastline level fresh SGD for the Crete Island in the Mediterranean Sea. The modeled hydrological processes suggested that fresh SGD substantially contributes to water flow entering the Mediterranean Sea (2.3 × 108 m3/yr), amounting to 31% of river discharge and 14% of precipitation. Spatially, fresh SGD varied from 2.4 m3/yr/m to 13.4 × 104 m3/yr/m, with an average of 2.6 × 103 m3/yr/m. The local maxima were commonly associated with river mouths reflecting larger hydraulic gradients and higher permeable structures. Temporally, fresh SGD was impacted by episodic precipitation in a delayed and prolonged pattern. We found that fresh SGD variability at the coastline segment level was compared to point measurements and fresh SGD magnitudes summered up to the catchment level were consistent with global products. Our results suggest the coupled surface–subsurface hydrologic modeling approach is a promising strategy to quantify and partition large-scale water budgets down to point observations that typically do not capture the full range of fresh SGD dynamics. Presented on: Journal of Hydrology