On a national scale, nutrients and suspended sediment loads are higher than before European settlement in more than 90% of the river lengths assessed, and are substantially modified in at least one-third of the river lengths that were assessed in every drainage division, except Tasmania.²³ A national comparison of water quality²⁴ against Australian water quality guidelines for fresh and marine waters²⁵ and the Queensland water quality guidelines²⁶ showed exceedences (of the slightly to moderately disturbed protection levels) in turbidity (Figure 4.5), electrical conductivity (salinity) (Figure 4.6), pH (Figure 4.7), total nitrogen (Figure 4.8) and total phosphorus (Figure 4.9) in parts of all drainage divisions. There is a general paucity of monitoring data on groundwater quality, except in places with very localised concerns; the emphasis here is therefore on surface water quality. River and wetland acidification does not appear to be a major national issue, although there are serious local acidification issues in some regions, such as that experienced by parts of the lower Murray River through the drought, and in waters draining salinised lands in the South-west Coast division,

Poor and very poor ratings for turbidity predominantly occurred in the inland areas of the North-east Coast and Murray–Darling drainage divisions. Possible causes include low rainfall and subsequent low flow; increased extraction; and the impacts of urbanisation, land clearing and agriculture. Turbidity levels throughout the South Australian Gulf, South-east Coast and Tasmania drainage divisions have remained low for the majority of sites, with good compliance across the divisions.

Available data identified exceedence of salinity guidelines predominantly along the eastern margin of the Murray–Darling, south-eastern portion of the North-east Coast, eastern portion of the South Australian Gulf and south-west of the South-west Coast drainage divisions.

Salinity has been a significant issue in the Murray–Darling Basin for a number of years. The upper reaches of parts of the Basin have, in the past, exported much more salt than that which is delivered by rainfall, indicating that land clearing has increased the mobilisation of salts from these catchments.²⁷

In 2009–10, the Independent Audit Group for Salinity, responsible for annual review of progress on implementing the Basin Salinity Management Strategy, reported that the Basin salinity target had been reached for the first time.²⁸ Their report attributed this success to delivery of low salinity water from upstream storages down the Murray River and the operation of salt interception schemes to reduce salt inflows from regional watertables.

The report also noted that:

• The long-term drought in the southern Basin has significantly affected the salinity of the region. The low river flows have increased salinity levels in the Lower Lakes and the Coorong, and decisions had to be made to manage the risks salinity posed to critical human water needs and the ecology of the region over the short term.
• The lack of high river flows for 14 years in the Murray River has meant that salt was not exported from the Basin and has most likely built up along the river valleys. Based on previous drought–flood cycles, river salinities following a high river flow may increase significantly.

The majority of sites in Western Australia (Indian Ocean and South-west Coast drainage divisions) rated very poorly for salinity. Elevated salinity in this area is likely to be caused by a number of inherent characteristics, such as naturally occurring saline soils, combined with anthropogenic influences, especially the legacy effects of land clearing.

The greatest contributors to degradation across the Murray–Darling division are disturbance to the catchment and changes to nutrient and suspended sediment loads; most reaches in the central and western part of the division were moderately modified. In contrast, an arc of reaches down the eastern side of the Basin were assessed as substantially modified. This was concluded to be largely the result of poor habitat, and nutrient and suspended sediment load conditions.¹⁴ For those parts of the division in New South Wales, mean daily salinity in streams was lower during 2006–09 than during the previous six years. This may have been due to the millennium drought, which limited the mobilisation of salts into streams. Stream phosphorus was regularly (>50% of the time) above trigger (guideline) values at most sites in the upper and middle reaches of the division’s major inland rivers in New South Wales.¹⁸ Trigger values are used in the Australian water quality guidelines to indicate a possible risk to the environmental value, with action needed to further investigate or fix the cause.

Within the Australian Capital Territory (ACT), reduced availability of water as a result of the drought, combined with the effects of the 2003 bushfire, led to poor surface water quality for the reporting period; however, the full extent of the water quality problem is unknown. The quality of water in the Murrumbidgee River leaving the ACT frequently failed the acceptable water quality limits. Water entering the ACT at Angle Crossing on the Murrumbidgee River is of a better standard, with minimal failures across the measured water quality parameters.²⁹

Across the southern section of the South-east Coast division, water quality reflected the degree of modification of the catchment. Improvements in total phosphorus and turbidity were attributed to drought rather than any long-term improvement.¹⁹ In the northern part of the division, some sites in the north-west of New South Wales exceeded the trigger values by an order of magnitude, with median total phosphorus levels of 0.5 milligrams per litre compared with a trigger value of 0.05 milligrams per litre.¹⁹

Stream nutrient and turbidity levels in the South Australian Gulf division were generally in fair to poor condition, but stable since the previous SoE reporting period. Groundwater quality was stable throughout most of the division, although nutrient levels remained poor in many regions, and salinity increased in some.²⁰

Most surface water quality indicators across the North-east Coast division were assessed as good (or of concern), rather than poor; the proportion of sites in poor condition has decreased considerably since 2003. The reasons for this improvement are not clear. During the past 10 years, nitrogen values frequently exceeded ecosystem protection guidelines in northern aquifers and the sand islands, but did not exceed health guidelines.²¹

The majority of sampling sites across the Tasmania division (37 of the 52 stream gauging sites; 71%) experienced no exceedences of the upper guideline salinity (electrical conductivity) value of 482 microsiemens per centimetre. Most monitoring sites are at the bottom of the catchment and hence are affected by agricultural activities upstream. The majority of sites had more than 80% of samples above the guideline value for total nitrogen of 0.48 micrograms per litre.¹⁷

The 2008 Statewide river water quality assessment for Western Australia³¹ reported on the status and trends of nine key water quality parameters (total nitrogen, total phosphorus, total suspended solids, total dissolved salts, dissolved organic carbon, dissolved oxygen, pH, turbidity and colour readings) for 255 sites from 23 basins (out of a total of 44) in Western Australia. All basins in the South-west Coast division were represented by at least one site. In general, water quality failed national guidelines for nutrients and salinity in these rivers. Recent monitoring data are relatively lacking for most sites in the Indian Ocean, North-western Plateau and Timor Sea divisions, and virtually no water quality data are available for the South-western Plateau division, where flows are small and highly seasonal.