Wetlands globally are under threat from land use intensification and climate change, with the extent and condition continuing to decline. This includes wetlands located within the Great Barrier Reef catchment area (GBRCA). Wetland condition within the GBRCA is monitored as part of the Paddock to Reef Wetland Condition Monitoring Program using a static baseline pre-development which utilises the Regional Ecosystem (RE) mapping (i.e., native vegetation associated with specific geomorphic processes, soil and geology) to compare remnant versus pre-clearing vegetation. The Fitzroy Basin, located within the GBRCA, is the largest river catchment which flows into the Great Barrier Reef (GBR) marine waters. Understanding wetland environmental histories and conditions is therefore important for both maintaining intrinsic wetland ecosystem services, as well as identifying changes in sedimentation and land use which may ultimately impact the GBR. Here we use a palaeoecological approach to reconstruct wetland histories of three wetlands within the Fitzroy Basin, Central Queensland: Lake Mary North, Tualka and Lake Murphy. Over the past ~1,000 years these wetlands have recorded climatic shifts due to the millennial climate controls El Niño/Southern Oscillation and the Little Ice Age (LIA) and also environmental variations from changes in land use intensification due to European settlement. In all records we find evidence of a post-LIA dry period, European fire suppression and increased sedimentation rates post European settlement due to a combination of drought conditions and changes in land use. In this research we validate the use of Regional Ecosystem classification and show the need for longer, site specific environmental records within the GBRCA. These records are then compared to identify long-term aggregation changes between both protected and non-protected wetlands.