In Japan, water-quality monitoring with the environmental dioxin standard of 1 pg-TEQ/L at basic monitoring points set in a border between operation-area water and normal water is necessary for removal operations for bottom sediments containing dioxins. This paper presents a technique for combining on-site graphitic carbon (GrC) solid-phase extraction and bioassay method for the simplification and facilitation of water-quality monitoring. Using this method, we conducted experiments at an actual sediment removal site. Comparative analyses using high-resolution GC/MS (HRGC–HRMS) between the dioxin concentrations detected using a GrC solid-phase extraction kit and the official analytical method yielded similar concentrations and distributions of isomers for detected PCDD/Fs and DL-PCBs. The GrC solid-phase extraction method is inferred to have capacity equal to official analytical method extraction. Toxicity equivalent concentrations estimated using DR-CALUX correlate with equivalent concentrations with HRGC/HRMS. No false positive or false negative result was obtained for the standard value 1 pg-TEQ/L.