Coastal ecosystems represent a highly dynamic interface for human interaction with environmental microbial assemblages. We examined the dynamics of a coastal microbial community inhabiting a highly impacted urban beach, using a high resolution (weekly), two-year duration time-series. Microbial assemblage structure was characterised using 16S rRNA amplicon sequencing and several pathogens and antibiotic resistance genes were targeted using qPCR. Microbial community composition was highly dynamic, with patterns often reflective of anthropogenic impacts. Specifically, several Operational Taxonomic Units (OTUs) exhibited pronounced peaks in relative abundance that exhibited both direct, and time-lagged, correlations to stormwater and sewage inputs. Among these were OTUs from the Arcobacter genus, a group including pathogens often associated with sewage and wastewater infrastructure.  Arcobacter relative abundance regularly increased from < 1% to > 70% of sequences within 1 week, with network analysis revealing links with stormwater and sewage. These anthropogenic impacts also led to 1-2 order of magnitude increases in the abundance of several antibiotic resistance genes, including genes conferring resistance to both high use front-line and last resort antibiotics.  Network analysis linked the occurrence of these genes to Arcobacter and several other putative pathogens. Finally, frequent peaks in abundance of potentially pathogenic endemic marine microbes, including members of the Vibrio genus, were observed, but rather than being correlated to stormwater or sewage, were linked to marine heat-waves. These observations demonstrate that coastal microbial assemblages are shaped by a range of anthropogenic forces and are characterised by intense peaks in the abundance of potentially pathogenic and antibiotic resistant microbes.