Mosquitoes are both vectors of disease and a hindrance to outdoor activities. Since its discovery in 1976, the larvicide Bacillus thuringiensis var. israelensis (Bti) has proven its effectiveness in controlling mosquito populations, with negligible environmental impact. We performed an integrated, 5-year study of the direct and indirect effects of Bacillus thuringiensis var. israelensis (Bti applied as VectoBac (R) WG) on phyto-plankton communities in the Camargue temporary wetlands of the French Mediterranean coast. Mosquito larvae are considered major algae predators, so a significant reduction in mosquito larval density (\textgreater80%) in natural wetlands due to Bti treatment could indirectly affect phytoplankton communities. Physical parameters and phytoplankton were sampled in the water of three temporary oligohaline pools between 2006 and 2011 in the following order: T0 = 1 day before treatment (control), T2 = 2 days after treatment, T5 = 5 days after treatment, T11 = 11 days after treatment. We found no negative effects of Bti treatments on total phytoplankton density and community diversity (Shannon's entropy and Pielou's evenness). However, we observed changes in the density of some taxonomic groups; Diatoms were replaced by drought-resistant algae typical of temporary wetlands. These results suggest that changes in phytoplankton community structure are largely driven by natural environmental factors and by the ecological complexity of these temporary wetlands.