The Great Barrier Reef (GBR) system encompasses the largest system of corals and related life forms anywhere in the world. The health of this extensive system, particularly the inshore area, is dependent on the relationship between the GBR and adjacent coastal catchments. The major impact of agricultural practices on the GBR is the degradation of water quality in receiving (rivers) waters, caused by increased inputs of nutrients, suspended sediments and other pollutants. For the past three years, the Great Barrier Reef Marine Park Authority (GBRMPA) has been involved with the co-ordination of a river-monitoring program, specifically targeting the sampling of rivers during flood events. Representative sites were set up along two North Queensland rivers, the Russell-Mulgrave and Barron Rivers. This monitoring program is run in conjunction with the Queensland Department of Natural Resources' Waterwatch program. The program involves intensive sampling of first flush, extreme flow and post flood conditions over the two rivers. Extreme flow conditions are sampled over a limited time span (48 hours) with trained volunteers at 4-hour intervals. Concentrations measured in the flood events are dependent on land use characteristic, and extent of flow. Concentrations of dissolved and particulate nutrients are higher if the extreme flow event is part of the first flush cycle. Concentrations of DIN and DIP measured before, during and after a major flood event suggest that there is a large storage of inorganic material within the Barron and Russell-Mulgrave agricultural subcatchments that move over a period of days, and perhaps weeks. This program created a forum in which GBRMPA liased with the Barron and Russell-Mulgrave community about the connectivity existing between the river and the Great Barrier Reef lagoon.