Pesticide residues are found ubiquitously in Queensland east coast and Great Barrier Reef (GBR) waterbodies. The highest concentrations, often above Australian guidelines, are found adjacent to and downstream of areas of intensive cropping, largely sugarcane cultivation and horticulture. Due to the iconic status of the GBR more information on pesticide levels, risk to ecosystems and management solutions are available than in other parts of Australia. Freshwater bodies being, in general, closer to the source of pesticide residues from intensive agriculture, have higher concentrations present than waterbodies further away from the agriculture e.g. estuarine and marine environments. As such pesticide residues present a higher risk in these waterbodies with a lowering of risk as ecosystems become further distant from the sources. Management of pesticides in Australia is a joint responsibility of the Australian and State governments. Management for environmental protection at the Australian level by the regulator, the Australian Pesticide and Veterinary Medicine Authority, has serious deficiencies in process and practice. However at the Queensland Government level action is being taken to reduce pesticide pollution of waterways, including research, monitoring, risk assessments and application of better pesticide application methods. However only limited progress is being made in reducing pesticide exposure. Given the large knowledge base of pesticide management methods available there is some hope that residue levels and risk to ecosystems can be reduced.