Nest form and nesting habitat are important for a bird's breeding success due to their influence on the risk of breeding failure. The Japanese Marsh Warbler Locustella pryeri, which breeds in wet grasslands under habitat management, builds three types of nests: deep-cup Type I, domed Type II without decoration, and domed Type III decorated with live grasses. Relationships among nest types, habitat management, and nesting microhabitat characteristics were examined in the Hotokenuma wetland in northern Japan. During the breeding seasons in 2007–2010, a total of 263 nesting attempts were monitored, and 16 Type I, 61 Type II, and 25 Type III nests were measured. Prescribed burning affected the determination of nest type, and warblers built Type III nests frequently after burning. The microhabitat around the nests differed among the three nest types. Type II nests were constructed in wet conditions with abundant dead understory vegetation. In contrast, Type III nests were built in dry conditions with abundant live understory vegetation. Type I nests showed characteristics intermediate between those of the two domed types and were also found in spots with abundant hard stems. Nest type, habitat management, and nesting microhabitat did not affect nest predation or breeding success. We conclude that nest type differs depending on the characteristics of the nesting habitat.