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The JJAS river heights at Hay (Fig. 2a) have clearly reduced variability over the 27-year period 1965–1991 compared with 1992–2018 (p-value = 0.005, Table 4). Despite the apparent decrease in the mean and variance of JJAS Murrumbidgee River heights at Hay from the 1960s, as shown by the low p-values (0.309, 0.332), respectively, for the 27-year intervals 1938–1964 to 1965–1991 (Table 4), the decrease is not statistically significant. However, the decrease is consistent with the suggestion that a change point occurred from the late 1950s between unregulated to regulated flow at Hay11.While the mean JJAS precipitation of the three catchment locations of Burrinjuck Dam, Blowering Dam and Tumut indicate a slight decrease in percentile extremes from the 1990s, with 2016 (due to September) only above the 95th percentile (Fig. 3), they exhibit no significant change in mean or variance based on the bootstrapped intervals JJAS 1964–1991 to 1992–2018. Consequently, the question arises of why the significant decrease in mean and variance of the JJAS Murrumbidgee River height at Wagga Wagga and in variance at Hay does not match a similar significant decrease in mean or variance of JJAS catchment rainfall. A rainfall decline in recent decades was found to be most pronounced in late autumn20,21 and that without sufficient autumn rainfall to moisten catchments in southern Australia, follow-up rainfall in winter cannot be efficiently converted to run-off and catchment inflows22. There have been statistically significant decreases in April–May mean precipitation at the catchment locations of Blowering Dam, Burrinjuck Dam and Tumut from 1964 to 1991 to 1992–2018 and also for the mean inflows to the two Dams (Table 4). Furthermore, as a result of the Millennium Drought (1997–2009), modelling experiments indicate that, starting from very dry conditions, the run-off response to rainfall only will return to the normal pre-drought conditions after about 10–20 years of average rainfall23. Therefore, the significant decrease in variance of Murrumbidgee River heights at Hay and in mean and variance at Wagga Wagga, is most likely due to the April–May reduced dam inflows and precipitation, and from average JJAS catchment precipitation since 1991. Any role played by water extraction for irrigation between Wagga Wagga and Hay, where irrigation is concentrated, is likely to be small owing to the highly significant mean river height reduction at Wagga Wagga which is upstream from Hay. However, irrigation, and other water usage, is sourced from the dams, so there is a long-term impact of irrigation over the months preceding JJAS on flows at Wagga Wagga, due to the reduction in water stored in the upstream dams. The dams integrate the water extracted for irrigation and all other usage since the last spill event, and therefore the extractions over an extended period can have an impact on when the dam will fill, and hence on the flows downstream, including Wagga Wagga. The minimum water level in the dams, which typically occurs near the end of Autumn, is due to the reduction in inflows (impacted by climate change), and extractions from the dam. Coupled with the tendency for a slower fill rate due to reduced inflows, this results in fewer spill events. As a consequence, there is a change in the distribution between spill events and irrigation releases, changing the frequency distribution of flows. This will be particularly the case for the JJAS period, as a delayed dam filling will have a major impact in dam levels in that period. Before the 1990s the river at Wagga Wagga and Hay reached flood level height or close to flood level height regularly in JJAS from precipitation-driven inflows regardless of the amount of water that was extracted (see Fig. 2a,b). Since the mid-1990s less water reaching Wagga Wagga has significantly reduced the river height owing to significantly decreased April–May and JJAS precipitation-driven inflows at the upstream catchment dams of Burrinjuck and Blowering Dams and significantly decreased mean precipitation at Tumut, which also represents the catchment area of Blowering Dam (Fig. 2c,d; Table 4). Moreover, there has been no overallocation or hoarding of water found in the southern MDB24. In a different southern MDB catchment study of the Millennium Drought 1997–2008, factors for a disproportionate reduction in rainfall run-off were reduced mean annual rainfall, less interannual variability of rainfall, changed seasonality of rainfall and lastly increased potential evaporation25. However, the last two factors mentioned have since become well established in the last decade with reference to the work in this study. It was suggested that a rainfall reduction alone does not explain the observed inflow reduction trend26. Even after a major rain event, the soils are so dry that they absorb more water than before the rain event, and less reaches the dams and rivers than on a wet catchment. In the last three decades it is unknown what the effect on run-off into dams and the Murrumbidgee river has been in JJAS from major rain events because, apart from August–September 2016, there have been no major catchment net inflows since 1991 (Fig. 2c,d). There were significant precipitation-driven inflows during SON 2010 which led to flood level exceedances at Wagga Wagga and Hay in December 2010. In June and July 1991 there was a series of rain-producing cut-off low pressure systems over inland NSW and the adjacent coast influencing the catchment, interspersed with persistent, precipitation-producing frontal systems embedded in the westerly airflow during July and August. Rain producing inland cut-off low pressure systems over southeast Australia are the main influence on enhancing JJAS rainfall totals8.Decreased JJAS precipitation in continental southeast Australia has been evident for at least the last two decades, as anticipated by climate scientists. The naturally periodic La Niña phenomenon provided spring and summer precipitation during much of 2010 to 2012, which ended the Millennium Drought (1997–2009). The only other recent widespread significant rainfall in southeast continental Australia was in August–September 2016 due to a negative phase of the Indian Ocean Dipole (IOD). A negative IOD phase typically is associated with wetter than normal spring conditions for southeast Australia7,8.Although the SAM is an atmospheric index with a time scale typically of a few weeks, an annual average SAM reconstruction shows that since the 1970s it is in its most positive state over at least the past 1000 years27. Prior to the 1990s soil wetness would have been in phase with the annual cycle of winter/spring peak rainfall, dry summer/early autumn and without a long term trend in SAM. However, because SAM has trended positive since the 1970s, the annual cycle of soil wetness of the MDB has been increasingly disrupted particularly since the Millennium Drought23 and there is also a potential long-term impact from groundwater systems28. This is supported by the most recent available annual area-averaged actual evapotranspiration and soil moisture deciles in Fig. 7a,b. These figures show the anomalously dry MDB catchment area in the period 2018–2019. In the southeast corner of the MDB, actual evapotranspiration is below average and soil moisture is very much below average.Figure 7Available at: http://www.bom.gov.au/water/nwa/2019/mdb/climateandwater/climateandwater.shtml.Annual deciles of actual evapotranspiration and soil moisture 2018–2019. Map of southeast Australia showing for the MDB region deciles during the 2018–2019 year for, (a) annual area-averaged actual evapotranspiration. Note the below average decile in the southeast corner of the MDB, and (b) annual area-averaged soil moisture. Note the very much below average decile in the southeast corner of the MDB. (Reproduced with permission under Creative Commons Attribution Licence 3.0 from the Australian Bureau of Meteorology.Full size imageTwo Supplementary Tables showing historical April–May (S1) and JJAS (S2) maximum river heights above flood level at Hay (6.7 m) in IPO phases indicate, as expected, more in negative IPO phases than positive phases and importantly a dissociation with the IPO resulting from none in the most recent negative phase from 1998 and the preceding positive phase after the early 1990s. The implication is that accelerated global warming since the 1990s has overwhelmed the influence of negative IPO on precipitation.The MDB plan, introduced from 201329 provided, for the first time, regulated allocations to environmental flows for ecosystem sustainability of rivers in southeast Australia such as the Murrumbidgee. However, the plan requires that each year on 1 July a fixed amount of water is locked in for future consumption, split three ways with the highest priority for human consumption and irrigation for permanent crops (e.g., fruit trees and nuts). The remaining allocations are split between non-permanent crops (e.g., cotton, rice) and environmental flow. A major issue is that the forecast net inflows upon which the allocations are based are the minimum inflows experienced in the 120 years up to the end of the twentieth century. However, as shown, even lower inflows have been experienced in the past two decades. It is not surprising that there is a significant decrease in the JJAS variance of the Murrumbidgee River height at Hay (p-value = 0.005) and both the JJAS mean and variance at Wagga Wagga from the periods 1965–1991 to 1992–2018 (mean p-value = 0.0044, variance p-value = 0.095; Table 4) since this period corresponds with the significantly reduced mean April–May catchment precipitation and mean April–May dam net inflows. The fact that there has been no significant change in the mean Murrumbidgee River height since 1991 is an indication that there has been a lack of major April-September rain events. The lack of significant catchment rainfall events from April to September is the reason for the reduction in the mean and variance of river heights at Wagga Wagga. Floods in April–May are rare along the Murrumbidgee River and the six years since 1874 in which April–May floods occurred at Hay prior to 1991 (Table 3), were dominated by precipitation that occurred as a result of mid-latitude interaction with either tropical or subtropical moisture, whereas the last flood that occurred in March 2012, was the result of a rain-producing tropical low pressure trough in the easterly wind regime that extended from northwest Australia to a low pressure centre in southern New South Wales near the Murrumbidgee catchment. Moreover, given the significant decline in April–May, Murrumbidgee catchment rainfall, JJAS run-off into the dams and Murrumbidgee River height at Wagga Wagga since 1991, the implication for water allocations of irrigated agriculture downstream from Wagga Wagga and for flood plain environmental flows required for sustainable wetlands downstream from Hay, will continue to be a problem. More

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