Understanding the flow of carbon through hyperalkaline lakes is a key means of understanding their biogeochemistry, sedimentology, and their paleoenvironmental and paleoclimatic records. Furthermore, understanding how mineral precipitation is regulated in these lakes can provide insights into how their sequestration of carbon can be managed. We report geophysical surveys of Mono Lake, California, USA, which show unanticipated geomorphological control on the recent/contemporary formation of lacustrine carbonate formations (“tufa”). Acquired shallow-penetration seismic data show a fault zone below the lake floor, but despite the regional evidence for geothermal waters rising up these fractures, we find no evidence for tufa precipitation at the surface exposure of this structure, either in the seismic data or in the swath bathymetry. However, we do find sub-lacustrine tufa columns in these data elsewhere, which is the first time these have been reported directly. We find and report on a strong link between column location and meteoric Ca supply to the lake, with the latter sourced either through surface runoff or groundwater. For example, a region close to a creek inlet has more frequent and larger tufa bodies, which grow at a wider depth range than another region far from an inlet but close to the fault. This demonstrates the importance of meteoric water ingress in regulating carbonate mineral formation in these basins, and raises the possibility that management of water within the catchment could be a means to enhance carbon capture in natural and artificial hyperalkaline lakes.