Fish may not speak, but changes to their assemblage, population structures and other fish health indicators can tell us a great deal about the current state of an aquatic ecosystem. Being abundant and responsive to changes in habitat conditions, fish present a useful biomonitoring tool for assessing ecosystem condition. Fish health indicators which respond to habitat degradation have been integrated into Multimetric Indices (MMIs) such as the Index of Biotic Integrity, and such MMIs are now widely used for environmental monitoring around the world. Within the Fitzroy Basin of Central Queensland, decades of land use including cattle grazing, cropping and mining activities have resulted in large impacts to fish habitats. Despite this, the effects of habitat degradation on the Fitzroy Basin’s freshwater fish populations remain poorly studied. Thus, the aim of this study was to identify indicators for integration into a novel MMI: the Fitzroy Basin Fish Health Index (FHI). Potential indicators for the FHI were tested over two years at 12 sites within the Fitzroy Basin. Several fish indicators were responsive to changes in water quality and habitat condition, including novel indicators developed using local fish species. For example, percentage abundances of Atheriniform fish species fell with increasing levels of several water and sediment pollutants, and vice versa for Clupeiform and Hypseleotrid species. Nine indicators in total were thus identified for inclusion into the FHI, which was then validated at 20 sites across the 11 freshwater catchments of the Fitzroy Basin. The novel FHI developed was able to distinguish between sites which were in degraded vs. more pristine conditions, and was also responsive to localised habitat disturbances. Overall, the FHI has a potential for integration into regular monitoring programs, and could aid in providing a better understanding of ecosystem condition throughout the Fitzroy Basin and beyond.