The type of water management and drainage system could be a potential reason for variation in malaria transmission in rice cultivation areas. To investigate this we have compared the population dynamics of Anopheles mosquitoes (Diptera, Culicidae) in rice plots with controlled and uncontrolled water depth, i.e. casiers and hors-casiers, respectively in the Office du Niger, Mali. We also compared malaria transmission in areas with mixed and casiers plots. Larval collection was performed fortnightly with the standard WHO dipping technique. Adult Anopheles were collected both by pyrethrum spray and landing catches. During the dry season rice cultivation cycle, the larval density in the hors-casier was significantly higher than in the casier plots. The larval peak in the casier plots was considerably smaller than the one in the hors-casier. During the rainy season, no significant difference was observed between the two plot types. However, larval densities begin to rise approximately one month earlier in the casier then in the hors-casier plots, and continued to increase trough the rice development phases until the grain filling/maturation phase, declining thereafter. In contrast, in the hors-casier rice plots larval density increased throughout the rice development. This difference was not significantly reflected in the adult vector density and man biting rate. However, high relative frequencies of Anopheles funestus, survival and entomological inoculation rates of An. gambiae s.l. were observed in the mixed plot sector.