Sedimentation rates over the last 100 years within two lagoons on the southeast coast of Australia, Lake Illawarra and St Georges Basin, have been quantified to determine the effects of catchment land use change and native vegetation clearance on infill rates, and spatial variations in the rate at which the estuaries have filled. Both catchments have similar lake and catchment area but have experience different degrees of modification due to land clearing for agriculture practices, urbanisation and industrialisation. Results indicate that in the heavily modified catchment of Lake Illawarra sedimentation rates close to fluvial deltas can be in excess of 16 mm/year, and between 2 and 4 mm/year in the adjacent central basin. This is approximately an order of magnitude greater than the pre-European rates. In contrast, at St Georges Basin, where the catchment has experienced much less modification, sedimentation rates in the central basin appear to have remained close to those prior to European settlement. However, sedimentation rates in the urbanized margin of St Georges Basin are relatively high (up to 4. 4 mm/year). This rapid modern sedimentation in the margin of the estuarine embayments has been detected in several other estuaries in the region. However the degree of sedimentation within the bay-head deltas, and more significantly in the central basin appears proportional to the degree clearance of native vegetation (forest) in the catchment, urban expansion and development of heavy industry in the respective catchment areas. © 2011 Springer Science+Business Media B.V.