We address the main methodologies for collecting aquatic insects in various aquatic ecosystems and habitat types, describing both field and laboratory procedures. Fourteen insect orders have aquatic forms and can live as larvae, nymphs, or adults in aquatic ecosystems. Special emphasis is presented for different habitat types, and methods for collecting, preparing, and identifying aquatic insects are described. The main methods to collect aquatic insects are described for lotic; lentic; hyporheic zone; spring; marine, brackish, and inland saltwater; phytotelmata; and hygropetric and madicolous habitats. We describe the main methods and materials for collecting aquatic insects in the field, including active (e.g., nets, dredges) and passive (e.g., drift samplers) techniques for larvae and flying adults. Laboratory procedures, specimen preparation, species identification, and conservation and curator issues are described, as well as conservation implications for aquatic insects.