Aquatic organisms detect chemical cues to sense the local environment, for example, to find a mate, locate food, and identify danger. Knowledge of chemical cues can be used in aquaculture, in practical applications such as controlling mating behavior to increase fertility, enhance feeding, and decrease stress; in fisheries, by catching selected species with low-cost artificial attractants; and to address maritime issues, by decreasing biofouling. Aquatic organisms also detect chemical cues related to global environmental changes, ocean acidification, and increases in ocean plastics, all of which can affect their chemosensory behaviors. Here we discuss the nature of chemical cues and chemosensory biology and ecology of aquatic organisms, and potential applications with an emphasis on sex pheromones in commercially important and well-studied animals, namely, decapod crustaceans and fish.