A capture–mark–release program was run for 3 years in a rice-growing area of the inner delta of the Niger River in central Mali to monitor population dynamics of a major pest species, the multimammate rat Mastomys huberti. The abundance pattern showed a phase of low-to-medium abundances (June 2000–March 2002) leading to a peak (October 2002) followed by a dramatic crash ending in total population disappearance induced by general flooding of the area in October 2003. Reproduction started well after the end of the rainy season, contrary to observations for this genus elsewhere. Survival was very low between the end of the rainy season and the middle of the dry season, then high during the rest of the dry season. The annual flood of the Niger River was found to have a major influence on population and spatial dynamics of M. huberti in this area by eliminating available ground surface in high-flood years, thus causing local extinction, and by delaying the onset of reproduction to the beginning of the dry season. Overall, the dynamics of multimammate rats in the inner delta of the Niger River appeared to be linked to rainfall and flooding patterns in a complex way. Maximum demographic growth appeared to be associated with intermediate levels of flood height, consistent with the intermediate disturbance hypothesis.