Carbonate geothermometry is a fundamental tool for quantitative assessment of the geothermal and geochemical evolution of diagenetic and hydrothermal systems, but it remains difficult to obtain accurate and precise formation temperatures of low-temperature calcite samples (below ~ 40 to 60 °C). Here, we apply three geothermometry methods (∆47-thermometry, nucleation-assisted fluid inclusion microthermometry—hereafter NA-FIM—and oxygen isotope thermometry) to slow-growing subaqueous calcite spar samples to cross-validate these methods down to 10 °C. Temperatures derived by NA-FIM and Δ47-thermometry agree within the 95% confidence interval, except for one sample. Regression analyses suggest that the real uncertainty of ∆47-thermometry exceeds the 1 SE analytical uncertainty and is around ± 6.6 °C for calcite spar that formed at 10–50 °C. The application of δ18O thermometry was limited to a few samples that contained sufficient primary fluid inclusions. It yielded broadly consistent results for two samples with two other geothermometers, and showed higher temperature for the third spar. We also found that calcite with steep rhombohedral morphologies is characteristic of low temperatures (11–13 °C), whereas blunt rhombohedra prevail in the 10–29 °C domain, and the scalenohedral habit dominates > 30 °C. This suggests that the calcite crystal morphology can be used to qualitatively distinguish between low- and higher-temperature calcite.