Microbial mats, dominated by cyanobacteria, cover 22,327 ha of the intertidal area of the Pilbara, yet remain largely unstudied. It is well accepted that the cyanobacteria and other microbes within these mats play a number of significant ecological roles including carbon and nitrogen fixation, Sulphur cycling, as well as nutrient and oxygen production. We set out to conduct in situ experiments to measure net primary production mats under various environmental conditions (light/ dark, extreme salinity, exposure to tidal inundation frequency). In conjunction with measures of primary production, we also measured chlorophyll, fluorescence and nutrient release from dry mats and after freshwater saturation. These in situ measures were set out across a gradient of anthropogenic disturbance across the Pilbara coastline, from the south of Exmouth Gulf where very little human pressures exist, up to Karratha which is a mining and industrial hotspot of Western Australia. This research displays key ecological roles of microbial mats in the Pilbara and how these vary with anthropogenic disturbance.