Benthic animals in aquatic ecosystems suffer from various anthropogenic pollutants. A challenge in risk assessment of chemicals in aquatic ecosystems (i.e. ecological risk assessment) has been to balance cost-efficiency and effectiveness in detecting early warning signals of chemicals. In this study, hyperspectral imaging and behavioural measurements were evaluated as novel applications for detecting chemical effects on benthic animals, and the reliability of the incidence of chironomid morphological deformities as a more traditional bioindicator of sediment ecotoxicity was assessed. Chironomid deformity experts (25) analysed an identical set of samples for deformities. Deformity assessments were highly subjective and inconsistent. Apparently, guidelines and criteria are needed to improve and ascertain the reliability of deformity analysis. Hyperspectral imaging was tested as a novel method to detect metal contamination of benthic macroinvertebrates using cadmium (Cd) as a model metal. No effects of Cd were observed on traditional toxicity endpoints, survival and number of morphological gill abnormalities in caddisfly larvae. In contrast, hyperspectral features revealed a weak association with Cd concentration indicating darkening of larval soft tissues at high Cd. Further development and testing of this method and of the imaging process in particular, are needed. Another novel method was based on a quadrupole impedance conversion-technique to record behavioural responses of animals. A Multispecies Freshwater Biomonitor (MFB), which utilizes this technique, enabled quantitative behavioural measurements of benthic larvae in sediment and in situ stream water exposures. MFB was found applicable for recording different behaviours, locomotion and ventilation of chironomid, mayfly and lamprey larvae, although no consistent behavioural responses in contaminated sediments or mine-impacted streams were detected.