Recent research into the sources of post-European settlement increases in sediment yield to the Great Barrier Reef World Heritage Area (GBRWHA) indicate that in most catchments the dominant erosion processes contributing elevated sediment are those associated with the sub-surface sources of bank, gully, and scald erosion (stripping of the soil A horizon). Gully erosion is likely to be the dominant sediment source in the major sediment yielding catchments to the GBR like the Burdekin, Fitzroy, Normanby and Herbert catchments, with a large proportion being the alluvial form, where the erosion is occurring into floodplain deposits. By definition the initiation, and potential control of these alluvial gullies, are inherently linked to riparian zone land management. Bank erosion is also a process that is integrally associated with riparian zone processes, and in catchments such as the Normanby is as significant a source as alluvial gully erosion. Evidence from the Normanby also indicates that the deposition of suspended sediment within the macrochannel is far more significant than previously assumed; a sink that to date has not been accounted for in most catchment sediment budgets. Management strategies aimed at managing water quality delivered to the GBRWHA have not focused to the extent that they need to be on sediment sources derived from the riparian zone, nor to the potential of this zone to mitigate sediment delivery through storage. In this paper we present evidence for the critical role of riparian zone management in reducing sediment inputs to the GBR and suggest a targeted program similar to the former Land and Water Australia Riparian Program, should be re-established for managing sediment runoff to the GBR.