Although interest in fish welfare is growing, little research has addressed the welfare of laboratory or ornamental fish. Our aim here was to evaluate the effects of handling fish with a scoop, where the fish remained submerged in water, compared to handling with a net. We investigated the effect of the scoop vs. a dip-net in three different species: three-spined sticklebacks (Gasterosteus aculeatus), Panamanian bishops (Brachyraphis episcopi) and rainbow trout (Oncorhynchus mykiss) using a variety of assays. The results demonstrate that keeping fish within water in a scoop while transferring them between tanks can, but not always, decrease the negative effects of handling on stress responses.