Abstract In genetic ecotoxicology or eco-genotoxicology, there is lack of well-validated systems which could demonstrate the utility of multiple endpoints in environmental quality assessment. For an evaluation of genotoxic potential of heterogeneous marine sediment samples collected from a small fishing harbour in the UK, an in vivo test system using embryo–larval stages of the common mussel, Mytilus edulis was validated against direct and indirect acting reference mutagens. The system appeared to be sensitive and reproducible for cytogenetic endpoints analysed (sister chromatid exchanges (SCEs) and chromosomal aberrations (CAbs)). Following validation and chemical characterisation of the environmental samples, multiple endpoints were measured. Determination of the maximum tolerated dose (MTD) was carried out as a measure to determine cytotoxic effects as a confounding factor for genotoxicity, based on developmental and cytotoxic (in terms of proliferative rate index or PRI) effects. Evaluation of the genotoxic potential of the samples gave a positive response for all the endpoints tested, linking different levels of biological organisation (i.e., chromosomal, cellular and organismal) for the observed effects. The study also emphasises the need for the assessment of the short and long-term impacts of dredge disposal on marine biota by including laboratory-based bioassays and incorporating an integrated approach which could yield as much useful information as possible in overall hazard and risk assessment for aquatic genotoxicity.