Calcite septarian concretions from the Permian Beaufort Group in the Maniamba Graben (NW Mozambique) allow controls on the composition and nature of diagenetic fluids to be investigated. The concretions formed in lacustrine siltstones, where they occur in spherical (1 to 70 cm in diameter) and columnar (up to 50 cm long) forms within three closely spaced, discrete beds totalling 2·5 m in thickness. Cementation began at an early stage of diagenesis and entrapped non-compacted burrows and calcified plant roots. The cylindrical concretions overgrew calcified vertical plant roots, which experienced shrinkage cracking after entrapment. Two generations of concretionary body cement and two generations of septarian crack infill are distinguished. The early generation in both cases is a low-Mn, Mg-rich calcite, whereas the later generation is a low-Mg, Mn-rich calcite. The change in chemistry is broadly consistent with a time (burial)-related transition from oxic to sub-oxic/anoxic conditions close to the sediment–water interface. Geochemical features of all types of cement were controlled by the sulphate-poor environment and by the absence of bacterial sulphate reduction. All types of cement present have δ13C ranging between 0‰ and −15‰(Vienna Peedee Belemnite, V-PDB), and highly variable and highly depleted δ18O (down to 14‰ Vienna Standard Mean Ocean Water, V-SMOW). The late generation of cement is most depleted in both 13C and 18O. The geochemical and isotopic patterns are best explained by interaction between surface oxic waters, pore waters and underground, 18O-depleted, reducing, ice-meltwaters accumulated in the underlying coal-bearing sediments during the Permian deglaciation. The invariant δ13C distribution across core-to-rim transects for each individual concretion is consistent with rapid lithification and involvement of a limited range of carbon sources derived via oxidation of buried plant material and from dissolved clastic carbonates. Syneresis of the cement during an advanced stage of lithification at early diagenesis is considered to be the cause of development of the septarian cracks. After cracking, the concretions retained a small volume of porosity, allowing infiltration of anoxic, Ba-bearing fluids, resulting in the formation of barite. The results obtained contribute to a better understanding of diagenetic processes at the shallow burial depths occurring in rift-bound, lacustrine depositional systems.