Microalgae are photosynthetic unicellular microorganisms that represent an extremely important component of the aquatic ecosystem productivity, diversity, and functioning. Moreover, these microorganisms, using a network of signals, interact with all the other organisms present in their environment. Signals are often secondary metabolites that play an important role in competition, defense, attraction, and signaling. These molecules are recognized for having bioactive properties, but some of them are still largely underexplored and underexploited. This Special Issue focuses on studies aimed to improve knowledge on microalgal ecology (diversity and dynamics) in aquatic ecosystems, as well as on their capacity to produce bioactive compounds with potential biotechnological applications.