Abstract Geothermal heat flow (GHF) data provide important constraints for ice‐sheet flow dynamics as GHF affects sliding conditions at the ice‐bed contact and englacial temperatures. However, marine measurements of the geothermal gradients can get distorted down to ∼3–10 m below seafloor by annual bottom water temperature variations. First‐ever geothermal data from the Bellingshausen Sea shelf, West Antarctica, are presumably affected by temperature variations in the modified Circumpolar Deep Water (mCDW) over annual and multidecadal periods. As magnitude and resolution of temperature data are low in the Bellingshausen Sea, we test a 1D water‐sediment model on Baltic Sea data, which includes long‐term water temperature and semiannual GHF measurements. The model approximates the measured sub‐bottom temperatures satisfactorily, although sparse data in Antarctica lead to uncertainties in reconstructed bottom water temperatures. Distortions in the geothermal gradients of the Bellingshausen Sea can be modeled using annual water temperature variations of ±0.03–0.15°C. However, the spatial heterogeneity of mCDW temperatures, recorded by heat flow lance sensors, shows no connection to geothermal gradient distortions. Therefore, the mCDW temperature variations are likely not strongly seasonal but are local changes of similar magnitude. Higher‐resolution water temperature records are needed to quantify uncertainties through annual water temperature variations in the current measurement‐derived GHF of 47–84 mWm −2 in Ronne Entrance and 21–57 mWm −2 in Eltanin Bay. Multidecadal ocean warming reduces the geothermal gradient by 16%–55% in the Bellingshausen Sea and leads to a reversed geothermal gradient in the Baltic Sea. This highlights the need to correct marine GHF for environmental factors. Plain Language Summary Geothermal heat flow provides important constraints for ice‐sheet flow dynamics as it affects the sliding conditions at the ice‐bed contact and the temperature profile of the ice. However, subseafloor temperature gradients can be distorted down to 3–10 m below seafloor due to the annual variations in water temperature. First‐ever geothermal data from the Bellingshausen Sea could be affected by temperature variations in the modified Circumpolar Deep Water (mCDW) over annual and multidecadal periods. A vertical 1‐D model including water and sediment temperatures was tested on Baltic Sea data, as these contain a 66‐year bottom water temperature time series and semiannual subseafloor temperatures. Model outcomes for the Bellingshausen Sea demonstrate that water temperature variations of ±0.03–0.15°C can explain the observed distorted geothermal gradients. Spatial analysis of the mCDW indicates that these water variations are likely local temperature variations and not a clearly defined seasonal water temperature signal. The model shows that uncertainties in measured geothermal gradients of the Bellingshausen Sea cannot be resolved due to low‐resolution annual water temperature data, and thus, uncertainties remain in heat flow estimates of 21–84 mWm −2 . Additionally, bottom water warming recorded over the last decades further contributes to a reduction in the measured geothermal gradient. Key Points Marine geothermal heat flow (GHF) modeling shows the limit of reconstructing bottom water and sediment temperature variations in data‐sparse areas First GHF measurements in the Bellingshausen Sea show temperature signals of local bottom water variations Climate change has reached the seafloor temperature gradients of the Baltic Sea and the Bellingshausen Sea (West Antarctica)