The distribution of contaminants is seldom homogeneous in aquatic systems and microniches within benthic sediments can make them particularly heterogeneous. Following exposure to ‘pulsed’ dissolved copper concentrations, toxicity to the epibenthic amphipod, Melita plumulosa, is best described by the time-averaged concentration. In this study we investigated the behavioural response of M. plumulosa, to contaminated marine sediments. Based on the rate at which the organism avoided contamination, we then investigated how toxic effects may occur through pulsed exposures to contaminated sediments. Four field-contaminated marine sediments were collected from the field and characterised as containing potentially toxic concentrations of metals. These sediments and one toxic copper-spiked sediment were used in 0.25 to 10 day exposure assays using 6-8 week old laboratory-cultured M. plumulosa. Initial assays showed that M. plumulosa avoided sediment, moving to clean sediments, as early as 6 h after exposures, with significant differences from controls after 24 and 48 h. This suggested that M. plumulosa is able to detect sediment contamination and choose to inhabit uncontaminated sediment. To explore the implications of this avoidance on the toxic effects elicited during migration across heterogeneous sediments, pulsed sediment exposure bioassays were performed. For sediments that were highly toxic during 10-day exposures, significant toxicity occurred when exposed for period of 2 × and 3 × 48 h, but not for exposures of 3 × 24 h or 1 × 48 h. The study demonstrated that M. plumulosa has the ability to detect and avoid contaminated sediment, and that the frequency and duration of contaminant pulses are important in determining any resulting mortality from the exposure.