The major water quality issue in the Hopkins River Basin is high salinity. Due to this, surface supplies are supplemented by groundwater and surface water imports. Low dissolved oxygen and medium nutrient levels are also a concern in the Basin. Water quality with respect to dissolved oxygen is generally moderate in the upper half of Mt Emu Creek and in Brucknell Creek. Available data for nutrient levels indicate that the nutrient status is low in the Hopkins River and medium in Brucknell Creek and the Merri River. As a result, the suitability of the water for aquatic life is affected. Turbidity levels are fairly low in the Basin’s major streams, indicating good quality, however, during winter, levels are often elevated in certain areas.
Surface water quality in the Portland Coast Basin is good with respect to catchment condition and suitability for aquatic life but high salinity is a major issue. Surface water quality with respect to salinity is poor in the major streams, with the exception of the Surry River, where salinity is slightly lower. This precludes use of surface water for extensive domestic supply. The high salinities in the base flow of the streams are an indication of elevated groundwater salinity and minor dry land salting.
In the Glenelg River Basin, high salinity is a problem in the major streams, as are high levels of colour. Therefore, it is generally unsuitable for domestic supply. Water quality in the Wannon River at Dunkeld is locally poor due to moderate levels of nutrients and associated stimulation of productivity. Salinities in the main river systems generally increase downstream and are especially high in the tributaries of the Glenelg and Wannon Rivers. Catchment condition is otherwise good and the water is generally suitable for aquatic life. With respect to dissolved oxygen levels, water quality in the Basin is generally moderate with the exception of the Wannon River at Dunkeld – where concentrations are particularly low.
(DWR, 1989)
Dry seasonal conditions throughout the entire region during 1998-99 resulted in sharp increases in salinity levels in many district lakes and wetlands. Limited or no runoff into many lakes and wetlands last winter has exacerbated the increases. For example, the normal seasonal fluctuation for Lake Linlithgow is 10 000 EC in winter and spring, rising to 16 000 EC in late autumn. During 1999, the lowest salinity levels recorded were 25 000 EC and peaked at 50 000 EC (seawater) in autumn (GHCMA, 1999). These dry seasonal conditions continued during 1999-00, resulting in many wetlands drying completely and sharp increases in EC levels resulting (to 45 000 EC at Lake Linlithgow prior drying in February 2000). Increased salinity levels were also recorded for Lake Bolac and Lake Burrumbeet during 1999-00. As a result the Glenelg-Hopkins Catchment Management Authority (external link) has funded 95 water quality projects in the region throughout 1999-00 (GHCMA, 2000a).
Nutrient Management:
From 1928 to 2000, algal blooms have been reported at 16 sites in the Glenelg-Hopkins Catchment Management Region at differing frequencies.
Recorded algal blooms at waterbodies and waterways in the Glenelg-Hopkins Catchment Management Region:
| Drainage Basin | Location | Algae | Comments |
| Glenelg | Dunkeld | Anabaena Oscillatoria | CuSO4 dosing CuSO4 dosing |
| Merino Basin | Phormidium | monitored | |
| Rocklands Reservoir | Botryococcus | monitored | |
| Hopkins | Alexander Lake | Anabaena and Microcystis | |
| Caramut Reservior | Chroococcus | monitored | |
| Caramut Water Supply | Ulothrix and Euglena | monitored | |
| Deep Lake | Microcystis | Warning signs | |
| Green Hill Lake, Ararat | Microcystis | Drinking, recreation facilities banned | |
| Hopkins River, Boonerah | Unicellular green | monitored | |
| Lake Burrumbeet | Microcystis and Oscillatoria | Closed to recreation | |
| Lake Cartcarrong | Anabaena | ||
| Lake Gellie | Oscillatoria | Warning signs | |
| Lake Gillear | Anabaena | Warning signs | |
| Lake Terrinallum | Oscillatoria | Warning signs | |
| Mt Ewen Reservoir | Anabaena | CuSO4 | |
| Tank Hill Reservoir | Struastrum | CuSO4 | |
| Portland | Aringa Reservoir | Anabaena | Closed to recreation |