The Billabong-Yanco-Colombo Creek system is a key natural asset within the Murray Catchment Management Authority’s region, recognised for natural, economic, social and cultural heritage values. The Murray CMA needed better knowledge of the condition of riparian vegetation within this system to assist with identifying NRM investment priorities. The Murray CMA had a broad understanding of the vegetation condition of these waterways which generally declined as they flowed west into more arid environments with cumulatively more water extraction. To build on this knowledge, a number of vegetation and habitat condition assessment parameters were chosen that were repeatable and that could be rapidly applied across a wide geographic area. The methods applied assessed vegetation cover, structure, diversity, health and habitat quality from the instream environment back out through the riparian zone. The results confirmed a general trend of decline downstream; however the range of assessment parameters provided a number of interesting results that were unexpected. While the vegetation condition project was being undertaken, fish surveys were in progress to collect information on the distribution, relative abundance, diversity and condition of fish communities throughout the same system. This paper also compares the riparian and instream condition results with the fish survey results. These comparisons are informing managers of priority actions for vegetation and waterway management to improve habitat provision for native fish.