Background Irrigation systems have been identified as one of the factors promoting malaria disease around agricultural farms in sub-Saharan Africa. However, if improved water management strategy is adopted during rice cultivation, it may help to reduce malaria cases among human population living around rice fields. This study aimed to assess the impact of the different irrigation practices on malaria transmission, as well as to evaluate the water management system that will best mitigate malaria transmission in Malanville, Benin. Methods Knowledge, Attitude and Practice (KAP) study was conducted on 104 households staying on and around the rice fields in Malanville. The study focused on the frequency of mosquito bites and preventive measures against malaria as well as soil preparation and rice planting methods. Mosquito larvae density was assessed in different water management system: continuous flooding (CF) or intermittent flooding (IF), deep tillage (DT) or minimal tillage (MT) and normal levelling (NL) or abnormal levelling (AL) in an experimental hut set-up. Larvae were collected using dipping methods and their density was determined. Results Three tillage systems, which include the use of tiller, plow and hoe, were identified on the rice field. Continuous flooding was the only irrigation system used by farmers. Retrospective data from Malanville Health Centre revealed higher malaria cases during rice production season, which was also confirmed by field participants. The density of Anopheles larvae was reduced by 80.8%, 30.8% and 40.7% (P = 0.000) during transplanting, tillering and maturation periods, respectively with intermittent flooding compared to continuous flooding. In addition, a clear reduction of larva density was observed with both intermittent flooding systems applied to minimal tillage (MT + IF + NL) and intermittent flooding applied to deep tillage (DT + IF + AL), showing that intermittent flooding could reduce the abundance of malaria vector in rice fields. Conclusion Recommending intermittent flooding technology for rice cultivation may not only be useful for water management but could also be an intentional strategy to control mosquitoes vector-borne diseases around rice farms.