Research suggested fish communities in the Swan and Canning rivers, from Mosman Park and upstream to the Swan Valley and Kent Street Weir, had improved since the mid-2000s.
The index measures estuary health by calculating the diversity and number of fish species in the rivers.
Water quality, seagrass growth and distribution, and a survey of foreshore conditions are also calculated.
Environment Minister Albert Jacob said the index was consistent with the pattern of good-fair condition assessments in previous years.
�In total, 35 species and more than 30,825 fish were caught and released in shallow waters and 21 species and 1601 fish were caught and returned in deeper waters by scientists,� he said.
�It is important to note that the number of species caught in deeper water was consistent with those in 2012 and 2013.
�However, the number of species recorded in shallower waters in 2014 was notably higher than the 29 species recorded in the previous two years.�
Mr Jacob said the rivers were under pressure from climate change, historical land use and development, but the fish community results showed the rivers were stable.
�This year�s results reflect high and stable salinity in the rivers, higher oxygen levels and the absence of algal blooms across much of the waterway,� he said.
�It�s true that some parts of the river system are healthier than others but the claim that the river is dead is just not supported by the science and monitoring.�