Stromatolites date back some 3.5 billion years and constitute the most common and conspicuous fossils through the Proterozoic. These organosedimentary structures decreased dramatically in diversity and abundance by the late Neoproterozoic, a phenomenon often ascribed to destructive grazing by newly evolved metazoans. We investigated the concurrent processes of microbial calcification and metazoan bioerosion in one of the few locations (Rio Mesquites, Cuatro Ciénegas, Coahuila, Mexico) where living freshwater stromatolites, formed by cyanobacteria and diatoms, coexist with significant populations of metazoan grazers. We used microsensor chemical profiling and monitoring of bulk water Ca2+ concentrations to determine calcification rates and their dependence on microbial metabolism. The bioerosive impact resulting from grazing by endemic hydrobiid gastropods was assessed by gravimetric quantification of carbonaceous faecal pellet production. Calcification was clearly light-dependent, reaching maximal rates (saturation) at low incident light intensity, and was surprisingly efficient, with O2/Ca2+ exchange ratios well above unity, and with absolute rates similar to those found in corals. However, the erosive action of grazing snails removed most of these carbonate inputs from the oncolites. Thus, a precarious balance between constructive and destructive geobiological processes was at play in the system. The fact that accretion barely exceeded bioerosion in an environment highly conducive to calcification supports the potential impact of faunal grazing as causal agent in the demise of stromatolites in the late Proterozoic. Our findings indicate that a search for fossil evidence of bioerosive grazing in the form of carbonaceous faecal pellets associated with fossil stromatolites may provide a means to test that hypothesis directly.