The Murray Irrigation Region Aquatic Ecosystem Monitoring Program was instigated in 2006 to determine baseline conditions in the rivers and creeks of the Murray Irrigation Region (Region) and then provided the capacity to measure trends in key components of river health (vegetation, fish, macroinvertebrates and water quality) over the longer term. Ten sites were selected from six water courses throughout the Murray Irrigation Region; two sites each on the Murray River, the Edward River, the Wakool River and Billabong Creek; and single sites on the Niemur River and Tuppal Creek. Justification of the site selection is detailed in the pilot study report (Gigney et al. 2007a) and protocols handbook (Gigney et al. 2007b). This is the fourth annual report of a proposed ten year monitoring program. It is also the final report due to the cancellation of funding for the monitoring program at the completion of the 2009 sampling. This report covers the sampling periods March 2009 (autumn) and October 2009 (spring). It details the current condition of the rivers and creeks in the Region, with particular reference to water quality, macroinvertebrates, fish and aquatic macrophytes. This report has been produced in the style of "Smartrivers" reports (L. Benson - Ecology Management) Pty Ltd.) as requested by Murray Irrigation Limited (Murray Irrigation). In the results section, each site is reported separately. The summary and overview (Section 3) provides some comparisons between sites and comparison to 2008 results.