Abstract. We conducted a field survey in the Krka River and its estuary (Croatia) in September 2014 to study the significance of submarine groundwater discharge (SGD) and derived nutrients. During the sampling period, the exchange time of the brackish water above the halocline in the Krka River Estuary (KRE) was calculated to be 8.3 ± 3.5 days. Three approaches of three end-member model, mass balance model and time series observation in tidal period based on Ra isotopes were used to evaluate the SGD fluxes in the KRE surface layer. We estimated the SGD flux to be (1.3–7.8) × 10⁵ m³ d⁻¹, which was approximately 2.7–16.1 % of the Krka River discharge into the estuary. By establishing the nutrient budgets in the KRE surface layer, SGD dominated the nutrient sources, followed by Krka River. SGD-derived dissolved inorganic nitrogen (DIN) and dissolved orthosilicate (DSi) contributed 26.8–68.6 % and 9.5–38.3 % to the total DIN and DSi fluxes into the surface waters of KRE, respectively. This indicates that SGD was likely a major external source of those nutrients in the KRE. We have identified that SGD-derived nutrients and their high N : P ratios may affect the ecosystem productivity in the KRE and nearby Adriatic.