A first study of the rotifers of the Niger River in Niger is reported here. Two surveys took place under contrasting hydrological conditions: low-water level (16 April to 8 May 2018) and high-water level (1 to 15 February 2019). Zooplankton and physico-chemical parameters were sampled at eight stations spread over 520 km from Ayorou to Gaya. In total, 32 taxa were identified, including 26 at species level. During the low-water sampling, Polyarthra sp. (31%), Brachionus caudatus (23%), Synchaeta longipes (11%), Keratella tropica (7%) and Filinia longiseta (5%) were the most abundant, whereas Brachionus quadridentatu s (26%), Lecane hastata (25%), Keratella cochlearis (9%), Keratella lunaris (5%), Hexarthra sp. (3%) were dominant during the high-water sampling. The mean abundance of rotifers ranged between 14 × 103 ind. m−3 during the high-water sampling and 244 × 103 ind. m−3 during the low-water sampling. The highest diversity was observed in the three stations located upstream from the city of Niamey. The results reflect the difference in environmental parameters between the downstream and upstream Niamey stations. RDA analyses showed that the main environmental factors explaining the distribution of rotifers were dissolved oxygen, orthophosphate and nitrate concentrations.