Lake Eildon and Goulburn Weir have significantly modified the Goulburn River's flow pattern. Due to the impact of water harvesting, lower flows now occur in the Goulburn River in winter and spring while higher flows occur in summer and autumn due to releases to meet irrigation and consumptive demands. This reverses what would happen naturally. The river flow regime is also affected by land use changes and by the construction of small dams and drainage schemes. Levees and other structures prevent water inundating the floodplain. Tributaries downstream of major infrastructure (such as Seven Creeks and the Broken River) help contribute natural flows to the Goulburn River in the lower reaches downstream of Goulburn Weir.
Environmental water in the Goulburn system is held by the VEWH, CEWH and MDBA as part of the Living Murray program. The CEWH is the largest holder of environmental water in the Goulburn system. Availability and use of Commonwealth environmental water is critical to achieving outcomes in the Goulburn River. Environmental water held on behalf of the Living Murray program may also assist in meeting objectives in the Goulburn system en route to icon sites in the Murray system.
Environmental water may need to be delivered through the Goulburn system to meet a downstream environmental objective. Where possible, these releases are managed to achieve outcomes in the Goulburn system before being reused downstream.
Environmental targets can also be met by water delivered from Lake Eildon to meet downstream demands in the River Murray (known as inter-valley transfers). Goulburn inter-valley transfers occur at times during the irrigation season, from spring to autumn. These flows may assist in achieving the desired environmental objectives without the need to release environmental water.
The priority reaches are reaches 4 and 5 (see below) in the lower Goulburn River as they are the most flow-stressed sections of the river. Delivery of environmental flows to these target reaches also provides benefits and meets some environmental targets in upstream reaches. The use of environmental water to target objectives above the Goulburn Weir (reaches 1–3) is limited as they receive significant flows for the purpose of transferring consumptive water from Lake Eildon to Waranga Basin. These flows often meet or exceed environmental flow targets in this part of the system for most of the year.