ABSTRACT1. A prototype Estuarine Fish Health Index (EFHI) using biological indicators from multiple levels of biological organization is described. Three test estuaries of similar size and morphology but with different development pressures were sampled for this purpose.2. The EFHI integrates the well established Estuarine Fish Community Index (EFCI) developed for South African estuaries, which uses fish community level metrics to assess estuarine condition, with stress responses measured at lower levels of biological organization.3. Four sub-organism level biomarkers were used: liver histopathology assessment, acetylcholinesterase and lipid peroxidase assays and an individual fish condition factor analysis. The data from these analyses and the results of the EFCI were integrated to determine if combining these inputs produces a more sensitive and predictive tool for assessing estuarine health than when used in isolation.4. Challenges and management applications of this new tool are explored and further studies to improve its prognostic capacity are suggested.