Quantification of submarine groundwater discharge (SGD) is essential for evaluating the vulnerability of coastal water bodies to groundwater pollution and for understanding water body material cycles response due to potential discharge of nutrients, organic compounds, or heavy metals. Here we present an environmental tracer‐based methodology for quantifying SGD into Knysna Estuary, South Africa. Both components of SGD, (1) fresh, terrestrial (FSGD) and (2) saline, recirculated (RSGD), were differentiated. We conducted an end‐member mixing analysis for radon (²²²Rn) and salinity time series of estuary water over two tidal cycles to determine fractions of seawater, riverwater, FSGD, and RSGD. The mixing analysis was treated as a constrained optimization problem for finding the end‐member mixing ratio that is producing the best fit to observations at every time step. Results revealed highest FSGD and RSGD fractions in the estuary during peak low tide. Over a 24 h time series, the portions of FSGD and RSGD in the estuary water were 0.2% and 0.8% near the estuary mouth and the FSGD/RSGD ratio was 1:3.3. We determined a median FSGD of 41,000 m³ d⁻¹ (1.4 m³ d⁻¹ per m shoreline) and a median RSGD of 135,000 m³ d⁻¹ (4.5 m³ d⁻¹ per m shoreline) which suggests that SGD exceeds river discharge by a factor of 1.0–2.1. By comparison to other sources, this implies that SGD is responsible for 28–73% of total DIN fluxes into Knysna Estuary.