Abstract: It has been obscure whether the pollution in the Three Gorges Reservoir (TGR) has impacts on the survival of fish that inhabit in the upstream of TGR, thus it is very important to monitor the pollution level and to investigate the toxic effects on fish early development. In this study, we collected surface water samples from three typical areas of the TGR, and employed the ICP-MS method to determine the concentrations of 13 typical heavy metals. We also evaluated the toxic effects by exposing zebrafish embryos (2h post-fertilization, hpf) to filtrated water samples until 168 hpf. The concentrations of 13 heavy metals in the TGR were all under the limits set by the environmental quality standards for surface water. We then examined the developmental endpoints, the transcription of several key genes in reproduction, in the synthesis of thyroid hormone, and in the neural development of fish. There were no significant differences in hatching, survival, and deformity rates between embryos exposed to the TGR water and the control group. However, zebrafish larvae exposed to TGR surface water showed reduced transcription of genes involved in reproduction (er , ar, and cyp19b), in the synthesis of thyroid hormone (tr , tsh , and dio) and in the neural development (1-tubulin, syn2a, and gap43), and the water from site 3 had the most profound effects. Our results suggested that there might not be considerable heavy metal pollution in the surface water of the TGR, and that the early development of fish might not be affected at this pollution level. Further study is needed to test whether the molecular-level alteration may have long-term effects on the development of individual fish.