Larviciding to control malaria was assessed in rural areas with extensive seasonal flooding. Larval and adult mosquitoes and malaria incidence were surveyed routinely in four 100-km(2) areas either side of the Gambia River. Baseline data were collected in 2005. Microbial larvicide was applied to all water bodies by hand application with water-dispersible granular formulations and corn granules weekly from May to November in two areas in 2006 and in the other two areas in 2007 in a cross-over design. The intervention was associated with a reduction in habitats with late stage anopheline larvae and an 88% reduction in larval densities (P < 0.001). The effect of the intervention on mosquito densities was not pronounced and was confounded by the distance of villages to the major breeding sites and year (P = 0.002). There was no reduction in clinical malaria or anemia. Ground applications of non-residual larvicides with simple equipment are not effective in riverine areas with extensive flooding, where many habitats are poorly demarcated, highly mobile, and inaccessible on foot.