The Twangiza–Namoya Gold Belt (TNGB) developed in a Proterozoic, variably composed sedimentary sequence that is associated with felsic and mafic igneous rocks. During polyphase tectono-metamorphic episodes the basement was exposed to repeated periods of heat influx that mobilised hydrothermal fluids and, at the Meso- to Neoproterozoic boundary, led to the formation of “G4” granites and pegmatites. The evolution of the TNGB hydrothermal system and its associated gold mineralisation are poorly understood. Here we investigate the tourmaline major elemental and the boron isotopic composition from one pegmatite and seven tourmaline-bearing hydrothermal veins sampled from the Kamituga and the Lugushwa gold deposits.Tourmalines from the hydrothermal veins are essentially dravitic with variable Ca contents. In contrast, the pegmatitic tourmaline is schorl–elbaite dominated and largely Ca-free. The boron isotopic signature of hydrothermal tourmaline from the Kamituga deposit (δ11B: −18.4‰ to −15.3‰) is distinctly lighter than that from Lugushwa (δ11B: −13.0‰ to −8.9‰). Pegmatitic tourmaline from Kamituga shows intermediate δ11B values between −14.2‰ and −13.1‰ with an average of −13.9‰. The pegmatitic fluid most likely had a δ11B composition in the range of −12.8‰. The isotopically significantly lighter boron in tourmaline from hydrothermal veins from Kamituga cannot have formed by fractionation from this pegmatitic source.Using the Rb–Sr mineral isochron method we have dated the Kamituga pegmatite as 981±16Ma, which correlates in time with the regional late-Kibaran “G4” granites. Tourmaline-bearing veins from Lugushwa are significantly younger and formed during the early stages of the Pan-African orogenic period (677±17Ma; Rb–Sr mineral data).Fluid inclusions in quartz that are texturally associated with hydrothermal tourmaline contain abundant saline brines and CO2-rich fluids that are commonly associated with CH4 and in places with amorphous carbon and N2. We interpret these fluids as having been derived from the hosting sedimentary sequence. This model is in agreement with the observed tourmaline composition, which are most readily affiliated with a variably Ca- and Al-rich pelitic source. Our model based on the isotopic, age and mineral compositional evidence indicates a sedimentary source of fluids forming the tourmaline-bearing hydrothermal veins in Kamituga and Lugushwa.