Recent studies recognized distinct stromatolite provinces in Hamelin Pool, Western Australia, each with morphologically distinct stromatolite structures paired with characteristic shelf physiography. In the present paper, we couple detailed lithofacies mapping with Hamelin Pool bathymetry and consider physiography as a control of sedimentation processes, including stromatolite development. Bathymetric transects, derived from a high-resolution bathymetry map with depths from 0 to 11 meters, allow calculation of slope gradients in the provinces. As in other settings, bathymetry is linked to energy regimes, which in turn appear to be coupled with variations in stromatolite morphologies and associated lithofacies as follows: (1) low-gradient ramps with low-energy settings are associated with sheet mats and elongate-clustered stromatolites that exhibit regular spatial patterns, possibly indicative of self-organization; (2) low gradients coupled with high-energy settings resulting from strong winds result in seif stromatolites with pronounced directional bands; (3) medium to steep gradients coupled with medium to high energy are associated with individual and merged stromatolites, often with thin basal necks; (4) headlands and promontories where the topography deflects currents are associated with elongate-nested stromatolites; and (5) medium- to high-energy slopes typically found at promontory edges and shelf margins are dominated by blocky pavement. Observations linking stromatolite morphology to physiography in a modern microbial system provide insight into the long-lived debate about biology versus environment in controlling stromatolite morphology. When physiography leads to a high-energy regime, environmental controls are the main factor determining stromatolite morphology. In contrast, when physiography promotes a low-energy environment, the response of biological communities becomes the main driver of macroscale stromatolite morphology.