Massive mosquito nuisance problems, caused by the flood-water mosquito Aedes sticticus, occur after floods in the flood plains of the River Dalälven, central Sweden. Since 2002, the biological mosquito larvicide Bacillus thuringiensis var. israelensis (Bti) has been used to control these mosquitoes. Here, we report results from the first six years of monitoring Chironomidae, the most susceptible non-target organisms, in three wetlands with Bti-treatment against mosquitoes and in three wetlands without treatment. Emergence traps were used for continuous insect sampling from May to September each year, 2002–2007, and were emptied once a week. A total of 21,394 chironomids of 135 species were collected, and the subfamily Orthocladiinae dominated the fauna followed by Chironominae and Tanypodinae. The annual chironomid production in the wetlands was low, with an average of 1917 individuals per m², and 42 g ash-free dry weight per m². We found no reduced production of chironomids at neither family, nor subfamily level, in Bti-treated as compared to untreated wetlands. This is the first long-term follow-up study of the possible effects of Bti-based mosquito larval control on chironomid species production. In the short-term view, one species had higher production in treated areas. In the long-term view, four species had higher and one species had lower production in treated areas. We conclude that the Bti-based control of flood-water mosquitoes does not cause any major direct negative effects on chironomid production, and therefore does not seem to induce any risk for indirect negative effects on birds, bats or any other predators feeding on chironomids.