This study investigated the dioxin-like (DL) PCB concentration and congener distributions in water, sediment, and Boleophthalmus pectinirostris samples collected from a beach near the 37th PCBs sealed site (the hazardous waste storage site was sealed by Zhejiang Province Environmental Monitoring Center) of Zhejiang Province, China, so as to evaluate the harmful effects of PCBs waste sealed sites on the surrounding environment. The results showed that DL-PCBs were in all samples. For all samples, the detection ratio of the mono-ortho congener PCB118 and the non-ortho congener PCB81 reached 100%, and both of their contents correlated well with the total DL-PCBs contents. Levels of low-chloride congeners were higher in environmental samples, while the enrichment of the high-chloride congeners was higher in fish. The content of PCBs in B. pectinirostris was highly related to the sediment environment, thus B. pectinirostris could well indicate environmental PCBs pollution. Considering both of the PCBs content and toxic analysis, even after 4 years of being excavated and cleaned, water, sediment, and fish samples were still at a certain degree of toxicity risks. Some areas were revealed to have a high toxicity risk, suggesting this PCBs sealed site still posed toxicity risks to the surrounding tidal flat ecosystem and might potentially endanger animals and human health.