Sulfate reducing bacteria (SRB) biostabilization has attracted particular attention due to its ability to prevent and control heavy metal pollution. In this study, biotic experiments (immobilisation test of Daphnia (D.) magna, germination experiment of cucumber seeds, and in vitro experiment using gut juices of Sipunculus (S.) nudus) and diffusive gradients in thin films (DGT) technique were performed to investigate the biosafety of cadmium (Cd) contaminated sediments after being treated by indigenous SRB. Results showed that SRB treatment reduced Cd bioaccessibility of sediment to S. nudus, Cd levels in the overlying water and Cd bioavailability to D. magna. However, the treatment increased the biotoxicity of overlying water due to significant reduction in the root length and germination index of cucumber seeds. DGT results confirmed that SRB treatment increased Cd stability in sediment, and reduced its release from the sediment into the overlying water. The biotoxicity of overlying water was not caused by Cd, but possibly by the added culture medium, SRB itself, or its metabolites. More attention is required to assess the safety of SRB treatment when it is used to remediate environmental matrix contaminated by heavy metals.