Aquatic insects having a high diversity are good biotic indicators for freshwater quality. Their larvae living in freshwater are sensitive to pesticides, and its impacts has been examined not only through laboratory toxicity studies using water and sediment exposure but also through higher-tier micro-/mesocosm studies and field monitoring. Many sophisticated statistical methods have been applied to assess the impacts of pesticides at levels from species to community, but their body burden has been studied much less, especially in relation to toxicity. We review the uptake, metabolism with relevant detoxifying enzymes, and depuration of pesticides in aquatic insect larvae, which determine their body burden and help to understand the toxicity profiles specific to each chemical class. We also discuss experimental conditions, environmental factors, and species sensitivity in relation to the bioconcentration/-accumulation and toxicity of pesticides.