Abstract: The lacustrine carbonate reservoirs of the South Atlantic host significant accumulations of chemically reactive and Al-free Mg-silicate minerals (e.g. stevensite, kerolite and talc). Petrographic data from units such as the Cretaceous Barra Velha Formation in the Santos Basin suggest that Mg-silicate minerals strongly influenced, and perhaps created, much of the observed secondary porosity. The diagenetic interactions between reactive Mg-silicate minerals and carbonate sediments are, however, poorly known. Here we develop a conceptual model for the origin of secondary porosity in the Barra Velha Formation guided by considerations of the chemistry that triggers Mg-silicate crystallization, as well as the geochemical and mineralogical factors that act as prerequisites for rapid Mg-silicate dissolution during early and late diagenesis. We conclude that sub-littoral zones of volcanically influenced rift lakes would have acted as the locus for widespread Mg-silicate accumulation and preservation. Organic-rich profundal sediments, however, would be especially prone to Mg-silicate dissolution and secondary porosity development. Here, organic matter diagenesis (especially methanogenesis) plays a major role in modifying the dissolved inorganic carbon budget and the pH of sediment porewaters, which preferentially destabilizes and then dissolves Mg-silicates. Together, the sedimentological, stratigraphic and geochemical predictions of the model explain many enigmatic features of the Barra Velha Formation, providing a novel framework for understanding how Mg-silicate–carbonate interactions might generate secondary porosity more broadly in other lacustrine carbonate reservoirs across the South Atlantic.