The 2.5 Ga stromatolitic dolostones from the Lower Transvaal Supergroup in the Kanye Basin (Botswana) pre-date the first iron deposits, recording conditions before the great oxidation event (GOE). These dolostones have been deposited within a shallow marine carbonate platform extending from Zimbabwe to South Africa. The Lower Transvaal Supergroup carbonates of the Kanye Basin have been affected by the circulation of metasomatic fluids related to emplacement of the Moshaneng Dolerites (1.9–2.1 Ga). Here, geochemical and petrographic characterization of the Lower Transvaal Supergroup stromatolites is presented to shed light onto i) the effect of metasomatic fluids on the geochemistry of ancient carbonates, and ii) the environmental conditions prevailing before the onset of the GOE in the epeiric seas along the western margins of the Kaapvaal Craton. The dolomites show high Fe an Mn contents (average 2000 ppm and 3500 ppm, respectively) and very low Na contents. The overall rare earth elements (REE) pattern of dolomite vary consistently across the different dolomite facies with a sensible increase of ∑REE in the altered dolomites. The overall REE patter lacks La, Ce and Gd anomalies (average 1, 0.91, 1.05 respectively) and shows an overall chondritic Y/Ho ratio. The Eu anomaly is slightly negative or absent in most of unaltered samples. A positive Eu anomaly (average 1.28) has been detected in samples altered by metasomatic fluids. The dolomite samples from Ramonnedi Formation show Fe and Mn enrichment typical of Precambrian carbonates. Petrographic and geochemical analyses reveal that dolomitization and incipient diagenesis have probably affected the platform carbonates inducing neomorphism and recrystallization (i.e. xenotopic and syntaxial dolomite). The dolomitization processes have mobilized Y giving rise to a near chondritic Y/Ho ratio. Evidences for circulation of hydrothermal fluids related to the intrusion of Moshaneng Igneous Complex and Moshaneng Dolerites are shown only in one sample. Most samples of stromatolitic dolostone have negative Eu anomaly suggesting deposition in a closed basin system restricted from open marine circulation.