Fish communities are important indicators of the health of riverine ecosystems. Fish monitoring for The Living Murray (TLM) initiative, one of Australia's most ambitious restoration undertakings for the degraded river-floodplain biota of the River Murray system (south-eastern Australia), was carried out annually from 2005 to 2011 across six 'Icon Sites', including the habitats and reaches therein. These spatial and temporal components of variation in fish community abundance and composition must be taken explicitly into account for consistent assessment of riverine ecosystem health. To address this requirement, a standardised analytical framework, consisting of a sampling design and appropriate statistical methods, is outlined in this study. Based on an extensive dataset, multivariate patterns and univariate trends in fish community structure were analysed to show the flexibility, modularity and ability of the framework. The applicability of the framework to Turkish riverine ecosystems is then discussed with emphasis on the need for participatory discussion between researchers and environmental managers. The possibility to incorporate other measures of fish health such as biomass and condition, and to extend the proposed framework to the quantitative assessment of vegetation and bird communities also exists.