The Fitzroy River Aqua-Eco Health Project is a collaborative research project between the Central Queensland University, the University of Queensland and BMA. It is designed to assess the aquatic ecology and health of the streams within the Fitzroy catchment located adjacent to mine sites. The universities are conducting an independent sampling program expected to yield the most comprehensive monitoring to date. The project design incorporates in situ testing of water quality variables including temperature, dissolved oxygen, conductivity, oxidation reduction potential, pH and turbidity. Water and sediment chemistry incorporate testing for sulfate, suspended solids, nutrients and metals. This sampling is complemented by quantifying changes in the abundance and diversity of a wide range of biota, including microbial, macro invertebrates and fish.This paper will detail the program and highlight some of the particular difficulties in conducting this type of research in ephemeral stream systems. Case study examples will be used to illustrate insights being gained from the program. CITATION:Fabbro, L D, Vink, S and Sellens, C, 2013. The Fitzroy Aqua-Eco Health Project, in Proceedings Water in Mining 2013, pp 117-120 (The Australasian Institute of Mining and Metallurgy: Melbourne).