Coastlines worldwide are experiencing unprecedented increases in human population and urbanisation, leading to the degradation and loss of marine habitats. Seagrass meadows are particularly susceptible to human impacts, and commonly undergo habitat fragmentation before permanent loss. The relationship between seagrass fragmentation and anthropogenic processes, however, remains unclear. We quantified the fragmentation of Posidonia australis meadows using detailed habitat maps from 10 New South Wales estuaries (populations are listed as endangered in six of these systems) to test for associations with urbanisation and related human disturbances. At the scale of entire estuaries, seagrass fragmentation was positively correlated with human population density within estuarine catchments. At local sites throughout estuaries, fragmentation was greatest in areas with a high number of artificial structures - which included boat moorings, jetties, and aquaculture leases. These findings provide a greater understanding on how humans are transforming seascapes by altering habitat extent and structural connectivity, and will assist management to identify vulnerable areas of seagrass meadows for conservation.