AbstractLake sediment volume calculation is a challenging task, namely in cases when detailed drilling is complicated, expensive, or impossible, information on the pre‐sedimentation surface unavailable, and record of siltation rate non‐existent or too short. This study shows how waterborne, non‐invasive geophysical survey, such as electrical resistivity tomography (ERT) can be very effective in acquiring the missing data, namely when combined with sound navigation ranging (SONAR) water depth measurements and supported by information from auxiliary sources. However, ERT surveying in water environment requires specific approaches, as we illustrate on the case of the Mladotice lake study. The lake was created after a landslide in May 1872, and since its formation, the depth has gradually decreased due to sedimentation. We have reconstructed the original surface, calculated the sediment volume, and compiled information on sedimentation to estimate its remaining life span. To achieve this, we measured nine waterborne ERT profiles across the lake. To reach the necessary depth, all ERT profiles were extended on land and crossed the lake using custom‐built flotation pads. ERT profiling was combined with SONAR depth measurements, historical bathymetric surveys, borehole core analysis, sediment flux measurements, volumetric calculations, and water conductivity probing. The study has achieved three main results. First, practical applicability and advantages of stationary waterborne ERT profiling in combination with bathymetric sounding were demonstrated. Second, the original lake volume and accumulated sediment was calculated. We estimate that the volume of lake sediment is 187 000 m3, two‐thirds of the original lake volume (over 275 000 m3). Finally, based on three volumetric data sets from 1972, 2003, and 2017, and recent monitoring of the sediment inflow, we propose scenarios of lake filling and its future development. Most interestingly, the sedimentation rate has decreased significantly in the last 20 years, suggesting that the lake may survive much longer than hitherto expected. © 2020 John Wiley & Sons, Ltd.