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Malaria is the most significant protozoan disease in Africa and the principal vector-borne disease (VBD) in Nigeria, which is influenced by the quality of breeding habitats that are reflected through the stage preceding adult. Control of Anopheles gambiae s.l. populations through source reduction is still considered the most effective way of prevention and control, although it has proven unsustainable in Niger State. Physico-chemical cues were investigated. Samples were taken inside and outside 1 m2 cages weekly by dipping and emptying the cages from May 2019 to March 2020. The data subjected to analysis of variance (one and two-way Anova). The findings revealed the mean pupae abundance (MPA), were significantly higher in Large Water bodies (624.50±217.81), and followed by Gutters (436.00±184.2) and Swamps (285.50±125.06). The mean pupae productivity (MPP), followed the order of descending rate>GT (717.50±219.38)>LW (677.21±145.10)>SW (530.40±136.97). The result also showed that emptying technique (ET) was more sufficient and reliable than dipping technique (DT). The peak abundance and productivity of the pupal stage was June to August then declined in March, 2020 both habitats. However, MPP differed significantly (p<0.05) from one another across the months in all the habitat types. The physical and chemical cues of the breeding sites, varied significantly, except in temperature, total hardness, biochemical oxygen demands, conductivity, and pH in all the habitats. This study revealed high utilization of physico-chemical properties and poses increased risk of malaria. Thus, emphasis on the vector management strategies should be given specially on gutters and large water bodies as breeding habitats of malaria vectors (MV), in Niger State. [ABSTRACT FROM AUTHOR]