Bacillus thuringiensis var. israelensis (Bti) is an effective larvicide to control mosquito populations, with negligible environmental impacts. Bti treatments raise the question of possible effects on food webs, with potential proliferations of phytoplankton due to mosquito elimination. We found no negative effects of Bti on total phytoplankton density and community diversity, though diatoms tended to be replaced by drought-resistant algae.