Although there are common indicator organisms and tissues used in metal exposure assessment, mostly liver and gills of fish, bivalves and crustaceans, we are still in need of reliable and sensitive bioindicators, which will reflect bioavailable and therefore, possible toxic metal level, but also short and long term metal changes in the aquatic environment. Although fish intestine was rarely used as bioindicator tissue, the current studies indicate that both diet- and waterborne metal uptake are of equal importance for native fish. Rare data on intestinal metal levels were mostly related to metal levels in fish intestinal parasites, acanthocephalans, which accumulate metals more effectively than other indicator organisms. So far, there is no data on dietary metal bioavailability and on mechanism of metal binding in acanthocephalans, so it is planned for the first time to estimate metabolically available metal fraction in fish intestine and gene expression in fish intestine and acanthocephalans under different metal exposure regimes. Research will be performed in the Krka River, as suitable ecosystem for evaluation of metal toxicity, accumulation and biological responses in organisms under different pollution impact, due to clean karst water but also industrial and municipal wastewater discharges. Organism responses will be estimated by biochemical and histopathological markers, as well as metal levels in brown trout intestine and muscle, acanthocephalans and calcified structures (otoliths, scales), which indicate long term metal exposure during fish growth. Besides native, experimental organisms (algae, Daphnia) will indicate possible toxicity of the river and wastewater by toxicity testing. Comprehensive evaluation of ecological state will include determination of metals in the water and sediment of the Krka River and four tributaries and for the first time 87Sr/86Sr isotope ratio, as a natural marker of geological characteristics.