This study outlines systematic order-of-magnitude differences between, on the one hand, consistent seepage measurements with inland hydrology-based estimates and, on the other hand, coastal-marine tracer-based estimates of submarine groundwater discharge (SGD) in different parts of the world. We investigate here, by different field case simulations, whether groundwater flow transience, caused by temporal variability on different time scales, may add a sufficient contribution to SGD from seawater intrusion (SWI) and re-circulation back into the sea to explain the major differences between different SGD estimation methods. The investigated temporal variability factors include tidal oscillation, and seasonal and long-term hydrological and water-use variability and change. Neither of these factors effects on SWI and its contribution to SGD could explain the major SGD estimation differences. A previously suggested explanation, regarding the neglect of tracer discharges into the sea through unmonitored near-coastal streams and river stretches in coastal-marine tracer-based SGD estimations, still goes much farther in identifying a main reason for the large SGD estimation differences by different methods.