We studied the fate of the brominated flame retardant hexabromocyclododecane (HBCDD) added in a particulate suspension to experimental ecosystems assembled from brackish (Baltic Sea) coastal bays. Two experiments examined how A) benthic macrofauna (over 21 d), and B) increased temperature (14 d), affected HBCDD concentrations and fractionation of α, β and γ diastereomers in the water, sediment and biota. A third experiment (C) run over three seasons (231 d), studied the effect of HBCDD dose on the same endpoints. In all treatments of the three experiments, HBCDD partitioned mainly to the sediment, and this proportion increased with time. Presence of macrofauna tended to increase the HBCDD concentration in the sediment and decreased its concentration in the water. Increased temperature (+5 °C) decreased the amount of HBCDD in sediment and water but not in the filter- and deposit-feeding infaunal bivalves (Macoma balthica). The partitioning between water, sediment and biota was not concentration dependent. In all treatments, sediment became enriched in γ-HBCDD, M. balthica in α-HBCDD and water in α- and β-HBCDD. Bioaccumulation of HBCDD in M. balthica was high in all experiments (logBSAF > 1.25), the α diastereomer contributing the most (logBSAF 2.1 to 5.2). There is a risk of trophic transfer of HBCDD from benthic to pelagic food webs, and secondary poisoning of marine consumers. This article is protected by copyright. All rights reserved.