Long-term trends of bottom-water concentrations of dissolved oxygen (DO), total nitrogen, and total phosphorus at 42 sites in Tokyo Bay were analyzed using monthly data from 1983 to 2018 measured by local government agencies. The results were visualized as spatial distribution maps. Bottom-water DO concentrations varied seasonally. The area of hypoxic bottom water (DO < 2 mg L −1 ) was greatest in September of every year. Examination of interannual variations of the spatial distribution of bottom-water DO concentrations in September revealed that along the eastern side of the bay, hypoxic zones have been shrinking since the mid-2000s, but along the western side of the bay, the bottom water closest to shore is hypoxic in September even today. The areal percentage of hypoxic bottom water during September within inner Tokyo Bay has declined from 30% around 2007 to < 15% around 2015 and has not changed since then. A comparison of the spatial distributions of the frequencies of occurrence of red tides (chlorophyll-a concentrations ≥ 50 μg L −1 ) and hypoxic water masses during 8-year intervals revealed that areas with high percentages of red tides coincided with areas with high percentages of hypoxic bottom water. The implication is that the reduction of the size of the hypoxic zones along the eastern side of the bay was due to less frequent occurrence of red tides there. Reducing the inputs of nutrients to the bay as a result of policies aimed at reducing water pollution has, therefore, contributed to the mitigation of the hypoxia problem.