Terrestrial catchments adjacent to the Great Barrier Reef have undergone extensive anthropogenic modification over the last 150 years, including substantial land clearing and land use change. From 1996 to 2006, rates of land clearing in Queensland were among the highest in the world. More than 60% of this clearing occurred within the Brigalow Belt bioregion, which includes 98% of the Fitzroy Basin and 46% of the Burdekin Basin, both of which drain directly into the Great Barrier Reef lagoon. This land clearing and land use change has led to increased pollutant loads of nutrients, sediment and pesticides entering the Great Barrier Reef, which adversely impact the survival of this precious ecosystem. Agricultural land use is currently the largest contributor to pollutant loads. The effects of land clearing and land use change on runoff in the Brigalow Belt bioregion are well documented. Long-term research has shown clearing of virgin brigalow scrub for cropping or grazed pasture has doubled runoff irrespective of land use. Peak runoff rates doubled when land was cleared for cropping and increased by 50% when cleared for grazed pasture. The short-term effects of land clearing and land use change on land resources such as soil fertility were also documented, but the long-term implications were not. It was unclear how these changes in hydrology and soil fertility as a result of land clearing and land use change impacted water quality. Contemporary water quality investigations seeking to address this question are confounded by multiple issues. For example, climatic variability in central Queensland is large, so long-term monitoring is essential to develop true systems understanding. Short-term, three-to-five-year monitoring programs often fail to capture extremes in climate, so findings may not translate temporally. Broad-scale land clearing in the Brigalow Belt bioregion of central Queensland commenced in the 1960s and was generally considered to have ceased in 2006. As such, contemporary water quality data sets, while reflective of current catchment condition, likely provide little insight into the magnitude of change in water quality immediately post clearing due to multi-decadal lags between clearing and monitoring. Larger catchment scale water quality studies can be further confounded by mixed land use within a catchment and mixed land management within a single land use. Both scenarios make it difficult to separate land use effects on water quality from land management effects on water quality, with one likely to mask the effects of the other. When broad-scale land clearing in the Brigalow Belt bioregion of central Queensland commenced in the 1960s, changes in hydrology and soil fertility were anticipated. In order to determine the effects of this land clearing and land use change on hydrology, soil fertility and productivity, the Brigalow Catchment Study was initiated in 1965. The subsequent data collected from this long-term paired, calibrated catchment study provided an opportunity to determine the impacts of land clearing and land use change on water quality. The use of long-term data from paired catchments of a single land use, that have been monitored for hydrological and soil fertility change since prior to clearing, resolves many of the confounding factors common to contemporary water quality studies. This study of the effects of land clearing and land use change on water quality had four objectives as follows:

1. To determine the impact of changing land use from virgin brigalow scrub into a crop or pasture system on runoff water quality;
2. To evaluate whether clearing of brigalow scrub for cropping or grazing would alter the dynamics of soil organic carbon, nitrogen, phosphorus, sulfur and potassium over time;
3. To determine the impact on water quality of managing grazing land by varying stocking rate; and
4. To determine the impact of managing grazing land with tebuthiuron, a herbicide used for broad-scale woody weed control in grazing systems, on water quality. All four of these objectives were priority knowledge gaps of the Reef 2050 Water Quality Improvement Plan 2017-2022, the 2017 Scientific Consensus Statement and their predecessors. Long-term water quality modelling indicated that changing land use from virgin brigalow scrub to cropping or grazing increased loads of total suspended solids, total and dissolved inorganic phosphorus, and ammonium nitrogen. The well-managed (unfertilised) pasture system had less nitrogen in runoff compared to runoff from virgin brigalow scrub. In years when runoff occurred from the agricultural catchments, but no runoff occurred from the virgin brigalow scrub, water quality loads were entirely anthropogenic and totally attributable to land use change. These changes in water quality were modelled by extrapolating data collected at least 17 years after land clearing and land use change. During this 17-year period, significant nutrient fluxes occurred within the surface 0.1 m of the soil profile associated with clearing, burning and subsequent agricultural production. These fluxes, in particular the nine-fold increase in ammonium-nitrogen, the eight-fold increase in nitrate-nitrogen and the two to three-fold increase in bicarbonate- and acid-extractable phosphorus immediately after clearing likely resulted in extremes in water quality loads and pollutant concentrations compared to that observed in later years. The effect of managing grazing land by varying stocking rate was greater than that of changing land use from virgin brigalow scrub to conservatively grazed pasture. Heavy grazing of improved pasture more than tripled runoff, peak runoff rate and total suspended solids loss compared to conservatively grazed pasture. Loads of total suspended solids, nitrogen and phosphorus in runoff were also greater from heavy than conservative grazing. The effect of land management on water quality was most easily determined where the input to the system was entirely anthropogenic, such as broad-scale application of herbicide. Unlike nutrients, with no confounding natural input, herbicide loss in runoff was entirely contingent on herbicide use. Tebuthiuron loss in runoff was primarily in the dissolved phase with no correlation to total suspended solids. Concentrations of tebuthiuron in runoff declined exponentially with time, cumulative rainfall and cumulative runoff. The new knowledge of the effects of land clearing, land use change and land management on soil fertility and runoff water quality generated in addressing the four objectives of this thesis has been extended, both spatially and temporally, by its inclusion in models for Great Barrier Reef catchments. This modelling estimates the effects of land management on water quality from catchments such as the Fitzroy Basin. Specifically, the research presented in this thesis has underpinned the design, calibration and validation of models at both the paddock and catchment scales as part of the Reef 2050 Water Quality Improvement Plan 2017-2022. This new body of knowledge has also been used to guide the development of regulations for protection of the Great Barrier Reef. These regulations were the focus of a 2020 senate inquiry, during which new knowledge from this thesis was presented in both written submissions and given as evidence.