A complex approach in characterisation of submarine groundwater discharge (SGD) off south-eastern Sicily comprising applications of radioactive and non-radioactive tracers, direct seepage measurements, geophysical surveys and a numerical modelling is presented. SGD fluxes in the Donnalucata boat basin were estimated by direct seepage measurements to be from 4 to 12 L s−1, which are comparable with the total SGD flux in the basin of 17 L s−1 obtained from radon measurements. The integrated SGD flux over the Donnalucata coast estimated on the basis of Ra isotopes was around 60 m3 s−1 per km of the coast. Spatial variations of SGD were observed in the Donnalucata boat basin, the average 222Rn activity concentration in seawater varied from ∼0.1 kBq m−3 to 3.7 kBq m−3 showing an inverse relationship with salinity. The continuous monitoring carried out at the site closest to the coast has revealed an inverse relationship of 222Rn activity concentration on the tide. The 222Rn concentrations in seawater varied from 2.3 kBq m−3 during high tides to 4.8 kBq m−3 during low tides, thus confirming an influence of the tide on submarine groundwater discharge. Stable isotopes (δ2H and δ18O) showed that SGD samples consist up to 50% of groundwater. Geo-electrical measurements showed a spatial variability of the salt/fresh water interface and its complex transformation in the coastal zone. The presented results imply that in the studied Donnalucata site there are at least two different sources of SGD, one superficial, represented by mixed fresh water and seawater, and the second one which originates in a deeper limestone aquifer.