Research priorities and themes for the MWRPP are co-developed (by the Waterway Ecosystem Research Group and Melbourne Water) through an annual workshop, conducted to identify:

1. Strategic research questions to be addressed;
2. Broad methods to address the research questions;
3. Potential research collaborators;
4. Potential avenues for funding of the research, including external opportunities; and
5. Desired outputs for knowledge dissemination.

This approach allows research projects to be tailored to meet the strategic priorities identified in the Water Plan, and those which occur as a result of unforeseen circumstances during a Water Plan period. The current set of research themes being pursued by the MWRPP are:

1. Waterway health planning tools;
2. Waterway hydrology and geomorphology;
3. Urban and rural stormwater management for waterway health;
4. Riparian and wetland vegetation management; and
5. Community participation in waterway management.