The catchment of Moreton Bay has been significantly modified since European settlement began in the 1820s, and these changes have not only changed the type of pollutants (nutrients and sediments) and the loading rates delivered to Moreton Bay, but also impacted on marine food webs and life cycles. This paper focuses on the major changes in water quality that have occurred in Moreton Bay during the past two decades (2000–2018). We analyse long-term water quality monitoring data and mud samples to determine the impact of catchment land-use changes and management efforts to reduce pollution over this period. While improvements in water quality have been observed in some parts of the Bay in response to management actions, water quality trends indicate that population growth and land development across the catchment is having a significant impact. Specifically, sediment and nitrogen loads threaten the health of Moreton Bay into the future and management of these pollutants is critical.