Embayments and the biota they support are highly susceptible to disturbance within adjacent catchments. Examining the timing and magnitude of impacts arising from human-induced disturbance in these systems is often limited due to the absence of long-term monitoring. Moreton Bay in south-eastern Queensland is a shallow embayment that receives inflows from a 21 220-km2 catchment. In this study, diatom abundances, pigment (chlorophyll-a, phaeopigments) and biogenic silica concentrations were evaluated in a composite sediment from central Moreton Bay to explore temporal trends in the photosynthetic community. The record extends from 1200 to 2011, incorporating the period of European settlement (c. 1840s) and rapid population growth and urbanisation of the catchment. The record shows that in central Moreton Bay bloom-forming marine diatoms (Thalassiosira, Thalassiothrix, Thalassionema) have increased in relative abundance since the mid-20th century, whereas the dominant benthic diatom (Paralia fenestrata) has declined. This transition most likely occurred in response to the compounding effects of increased delivery of nitrogen, fine sediments and pollutants to Moreton Bay as a consequence of changes in land use. The inferred historical decline in relative contributions of benthic microalgae to total primary production in central Moreton Bay has likely had wide-ranging ecological effects.