Submarine groundwater discharge (SGD) is a significant source of biogenic elements in estuaries, and relevant studies in karstic estuaries are scarce. Krka River Estuary (KRE), located on the eastern Adriatic Sea (Croatia), is a typical oligotrophic stratified karstic estuary. In this study, based on ²²⁶Ra and ²²⁸Ra, the total SGD flux into the KRE surface layer was estimated to be (12.8–16.2) × 10⁵ m³/day. A conservative estimation of the fresh groundwater flux was (5.0–8.3) × 10⁵ m³/day, which accounts for 10–17% of the Krka River discharge into the estuary. By establishing water and nutrient budgets in the KRE surface layer, we found that SGD dominated the nutrient sources, although it accounted for a small portion of the total inflow water. Specifically, net SGD‐derived dissolved inorganic nitrogen (DIN) and silicates contributed 58–90% and 24–64%, respectively, to the total input fluxes. These results indicate that SGD was a major external nutrient source, in which net SGD‐derived high DIN flux and high DIN to dissolved inorganic phosphorus ratio may affect productivity in the KRE ecosystem and nearby Adriatic Sea. Additionally, net SGD‐derived dissolved inorganic carbon (DIC) flux in the KRE (1.53 mol · m² · day) was much higher than those in most estuaries worldwide, suggesting that the DIC‐enriched karst aquifers are important sources for global carbon cycle. Therefore, the impact of net SGD‐derived DIC from karst aquifers on coastal seas will likely become more evident and substantial with further development of global climate change, such as sea level rise.