Storm disturbance and recovery of the peritidal benthic microbial ecosystem occurs as part of the natural climate regime in Shark Bay. However, tropical cyclone and winter storm frequency and intensity are known to be changing due to climate forcing. Presented here is an analysis of the biogeomorphic response of the benthic microbial ecosystem within the intertidal to upper subtidal zone and the beach face coquina deposits of Hamelin Pool, to the passage of Category 3 Severe Tropical Cyclone Olwyn (13 March 2015). Storm effects (initial response to 40 days post-event) include: erosional sculpting of sediments, mats and structures; deposition and winnowing of sediments; accumulation of mucilaginous products into flocs, slurries and sludges; along with limited development of new coquina deposits in the beach face. Medium (15 months) term observations include: mat recovery and changes with transformation of mucilage deposits into new subtidal gelatinous mats, intertidal transitional mats and low-elevation microbial structures. Observations suggest that this disturbance had both positive (the floc-to-mat biogeomorphic storm response) and negative feedbacks (enhanced bioturbation), which impact the development of stromatolite forming microbial mats and microbialite structures.