There are 114 coastal wastewater treatment plant (WWTP) outfalls in Australia, comprising a range of treatment levels, discharge volumes and environmental contexts, but it is unclear to what extent they threaten marine ecosystems. We used a spatially-structured sampling design in a retentive receiving environment to determine the distribution of residual contaminants and ecological effects on microbes around a WWTP outfall. Concentrations of nutrients, metals, antibiotics and PFAS were substantially lower in seawater at the outfall compared to effluent prior to discharge, but some metals (Cr, Cu, Zn), including total mercury, as well as PFOS, exceeded guideline values. Microplastics were most abundant 20 m away from the outfall, while nutrients and PFAS attenuated with distance from the outfall. Measurable changes in the marine microbial community could be attributed to the WWTP. While the abundance of microbial populations revealed only weak effects of WWTP discharge, DNA sequencing approaches revealed significant spatial changes in the microbial community that, in seawater samples, could be linked to the input of high phosphorus and PFAS concentrations within WWTP effluent. There was clear partitioning of the sediment microbial assemblage with distance from the outfall, but no clear association with any of the contaminants or environmental parameters measured.