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Nongmahir reservoir of Meghalaya state of northeast India (NEI), sampled at the littoral and limnetic regions, revealed fairly biodiverse zooplankton of total 56 species with peak consortium (52 species) in January collection from the littoral region. The richness indicated spatial monthly variations and heterogeneity at the two regions mainly influenced by Rotifera. The ‘soft and de-mineralized waters’ resulted in low zooplankton abundance. Copepoda > Rotifera with Cyclopidae > Brachionidae influenced zooplankton, and Mesocyclops leuckarti > Keratella cochlearis > Ascomorpha ovalis > Microcyclops hyalinus are notable species at the littoral region. The limnetic region recorded Rotifera dominance, and importance of Brachionidae > Cyclopidae and K. cochlearis > Conochilus unicornis >M. leuckarti >A. ovalis > Asplanchna priodonta > Polyarthra vulgaris. Zooplankton recorded moderate species diversity and notable differences of evenness and dominance. The spatial monthly differences of richness, abundance and diversity indices of zooplankton, and importance of notable taxa are hypothesised to habitat heterogeneity of the two regions. Our results also indicated limited and differential influence of individual abiotic factors on zooplankton taxa, while the canonical correspondence analysis registered high cumulative influence of 10 abiotic factors on the littoral (80.62%) and limnetic (74.79%) assemblages along axis 1 and 2. This study highlighted distinct temporal variations of different diversity parameters than our preliminary survey of June 1995–May 1996.