INTRODUCTION: Several studies have unravelled the linkages between malaria and macro-sized water bodies (lakes, dams, irrigations) in various parts of tropical Africa. However, those findings cannot be extrapolated to areas where micro-sized rainwater harvesting (RWH) ponds are dominant. This article reveals the linkages between malaria and RWH in some parts of central Ethiopia where micro-level irrigation is practised. METHODOLOGY: A descriptive study was conducted in five sample districts of Amhara and Oromia states. Systematic random sampling was employed to select 300 households. Data were collected using household survey, focus group discussion and key informant interview techniques. RESULTS: The launch of RWH in the surveyed area, coupled with warming regional temperatures, has created breeding pools for mosquitoes and a longer malaria transmission period. The location of RWH ponds, the type of pond covers in use, and the limitations of some government policies are among the factors respondents believe have lead to an expansion of malaria incidence in recent years. Users and non-users of RWH varied on the malaria-RWH nexus, which could be attributed to RWH-induced socioeconomic differences. CONCLUSIONS: Given the growing need for micro-level irrigated agriculture to feed a rapidly growing tropical population, coupled with a predicted warming of global and regional air temperatures, this study suggests a need for further investigation on a broader scale.