Environmental parameters in Hamelin Pool, Shark Bay were investigated to characterize extrinsic factors that may be affecting stromatolite morphogenesis. Hamelin Pool, which evolved into a restricted environment during the last few millennia, sustains the world's most extensive and diverse assemblage of modern marine stromatolites. These stromatolites occur in a shallow nearshore facies belt covering over 100 km of coast. Temperature, salinity, water level, and current data collected between 2012 and 2014 have revealed previously undocumented regional and seasonal trends. Regional trends include increasing salinity, greater temperature range, and decreasing energy moving southward from Faure Sill and to the Nilemah Embayment. Seasonal trends reveal paradoxically increased salinities in wet winter months and decreased salinity in dry summer months. When paired with annual tidal cycles, these trends suggest the influx of low salinity groundwater along the Hamelin Pool shelf. Speculation on how the documented environmental parameters may affect stromatolite growth suggests potential impact on morphology, internal fabric, and stromatolite-building microbial communities. These insights into environmental pressures within a living stromatolite system provide a framework for understanding extrinsic factors affecting microbial communities and stromatolite development throughout Earth history.