The objective of this study was to determine the effects of transported hypoxic water on macrobenthic species composition in Isahaya Bay, Kyushu, Japan. To this end, we conducted a field survey of water quality, sediment quality, and the macrobenthic community across seasons. Hypoxic intensity, defined as the percentage of the time that a region exhibits hypoxic conditions [dissolved oxygen (DO) &lt
3.0 mg L−1], was calculated for the summer period from July 1 to September 30, 2014 based on continuous monitoring data derived from six monitoring towers in the bay. Here, we discuss how the hypoxia-induced damage, defined as the change in the species compositions of the macrobenthic communities in the bay due to hypoxia, differs between the inner and middle regions of the bay (with muddy sediment) and the outer regions of the bay (with sandy sediment). A decrease in the density of macrobenthic species that was correlated to the period of lowest DO concentration (&lt
1.0 mg L−1) was observed in the inner region of the bay. A large number of species disappeared from the macrobenthic community in the outer region after the DO concentration had dropped to its lowest level, even though this region presented the lowest hypoxic intensity (6.6%). The species that disappeared, including crustaceans and some polychaetes, were presumed to be sensitive to, and to have escaped from, hypoxia. Fewer species disappeared from the inner and intermediate regions of the bay, which had high hypoxic intensities of 14.0 and 26.7%, respectively, than from the outer region. The reason for this appeared to be a predominance of hypoxia-tolerant species in the inner and intermediate regions but not in the outer region. Our study suggests that estimating the effect of hypoxia in a spatially heterogeneous environment must be done with caution.