Tone River (利根川) is one of the rivers in the Japanese Archipelago. Kamisu 66 is built around its banks, and the river serves as the water source for Kamisu 66's vast waterway network and irrigation.
In the 19th century, an ambitious waterworks project was started by Tokugawa Ieyasu to divert much of the water flowing into the seat of the Tokugawa Shogunate, Edo (which eventually becomes Tokyo) into the Tone River basin, artificially making Tone River the longest river in Japan.
In this configuration, the river generally flow east-south-east through the Kanto plain, making a slight south-south-east turn at Kamisu, almost parallel to the coast, just before it empties into the Pacific Ocean. Kamisu 66 therefore was built around this area as the villages are described as being in the "east" or "west" side of the river.
Kasumigaura Lake is a series of lakes located just upstream of Kamisu (and later Kamisu 66), with its outflow split between entering the Tone River and directly to the ocean. Originally an arm of an inland sea receiving salt water from the ocean, 19th century irrigation projects cut the lakes off from the ocean, turning it into a freshwater lake.
In the millenia following the collapse of the Golden Age, the river basin saw some significant changes. More rivers that previously flowed south into Tokyo Bay were diverted into the Tone River basin, since Tokyo became a wasteland and don't require the water, and the river swelled even more. To control flooding, a canal diverted some of the Tone's waters into Lake Kasumigaura, enlarging it and surpassing Lake Biwa in Kansai to become the largest lake in Japan. The smell of the lake as noted in the story indicate that algal blooms is apparently still a problem.