Trace element cycling within subterranean estuaries frequently alters the chemical signature of groundwater and may ultimately control the total chemical load to the coastal ocean associated with submarine groundwater discharge. Globally, karst landscapes occur over 12% of all coastlines. Subterranean estuaries in these regions are highly permeable, resulting in rapid infiltration of precipitation and transport of groundwater to the coast, and the predominant carbonate minerals are readily soluble. We studied the chemical cycling of barium (Ba), strontium (Sr), manganese (Mn), uranium (U), calcium (Ca) and radium (Ra) within the carbonate karst subterranean estuary of the Yucatan Peninsula, which is characterized by a terrestrial groundwater lens overlying marine groundwater intrusion with active submarine discharge through coastal springs. Terrestrial groundwater calcium (1–5 mmol kg−1) and alkalinity (3–8 mmol kg−1) are enriched over that predicted by equilibrium between recharging precipitation and calcite, which can be accounted for by groundwater organic matter respiration and subsequent dissolution of calcite, dolomite and gypsum. There is a close agreement between the observed terrestrial groundwater Sr/Ca, Mn/Ca, Ba/Ca and Ra/Ca and that predicted by equilibrium dissolution of calcite, thus the trace element content of terrestrial groundwater is largely determined by mineral dissolution. Subsequent mixing between terrestrial groundwater and the ocean within the actively discharging springs is characterized by conservative mixing of Sr, Mn, Ba and Ca, while U is variable and Ra displays a large enrichment (salinity: 1.9–34.9, Ba: 60–300 nmol kg−1, Sr: 15–110 μmol kg−1, U: 0.3–35 nmol kg−1, Mn: 0.3–200 nmol kg−1, Ca: 4.3–12.9 mmol kg−1, 226Ra: 18–2140 dpm 100 L−1). The deep groundwater sampled through cenotes, local dissolution features, is typified by elevated Ba, Sr, Ca, Mn and Ra and the absence of U within marine groundwater, due to enhanced dissolution of the aquifer matrix following organic matter degradation and redox processes including sulfate reduction (salinity: 0.2–36.6, Ba: 7–1630 nmol kg−1, Sr: 1.3–210 μmol kg−1, U: 0.3–18 nmol kg−1, Mn: 0.6–2600 nmol kg−1, Ca: 2.1–15.2 mmol kg−1, 226Ra 20–5120 dpm 100 L−1). However, there is no evidence in the spring geochemistry that deep marine groundwater within this reaction zone exchanges with the coastal ocean via spring discharge. Total submarine groundwater discharge rates calculated from radium tracers are 40–95 m3 m−1 d−1, with terrestrial discharge contributing 75 ± 25% of the total. Global estimates of chemical loading from karst subterranean estuaries suggest Sr and U fluxes are potentially 15–28% and 7–33% of total ocean inputs (8.2–15.3 mol y−1 and 4.0–7.7 mol y−1), respectively. Radium-226 inputs from karst subterranean estuaries are 34–50 times river inputs (6.7–9.9 × 1016 dpm y−1).