An integrated assessment of biological activity and ecotoxicity of fluvial sediments in the Marcal river catchment (3078 km²), western Hungary, is presented following the accidental spill of bauxite processing residue (red mud) in Ajka. Red mud contaminated sediments are characterised by elevated pH, elevated trace element concentrations (e.g. As, Co, Cr, V), high exchangeable Na, and induce an adverse effect on test species across a range of trophic levels. While background contamination of the river system is highlighted by adverse effects on some test species at sites unaffected by red mud, the most pronounced toxic effects apparent in Vibrio fischeri bioluminescence inhibition, Lemna minor bioassay and Sinapis alba root and shoot growth occur at red mud depositional hotspots in the lower Torna Creek and upper Marcal. Heterocypris incongruens bioassays show no clear patterns, although the most red mud-rich sites do exert an adverse effect. Red mud does however appear to induce an increase in the density of aerobic and facultative anaerobic bacterial communities when compared with unaffected sediments and reference sites. Given the volume of material released in the spill, it is encouraging that the signal of the red mud on aquatic biota is visible at a relatively small number of sites. Gypsum-affected samples appear to induce an adverse effect in some bioassays (Sinapis alba and Heterocypris incongruens), which may be a feature of fine grain size, limited nutrient supply and greater availability of trace contaminants in the channel reaches that are subject to intense gypsum dosing. Implications for monitoring and management of the spill are discussed.