Over the last few decades, the contribution of aquaculture to animal protein production has increased enormously, and the sector now provides almost half of the fish and shellfish consumed worldwide, making it a major food producer. Nevertheless, many factors, including infections, pollution, and stress, may result in significant economic losses. The aquaculture industry will not be totally successful without the therapeutic and preventive means to control all these factors. Antibiotics (long used in aquaculture practice) have tended to aggravate the problem by increasing antibiotic resistance. Concomitantly, probiotics have widely been suggested as eco-friendly alternatives to antibiotics. However, the way in which probiotics are applied in aquaculture is a key factor in their favorable performance. The aim of this review was to examine the current state of probiotics administration through the water in finfish aquaculture. The review also attempts to cover the research gaps existing in our knowledge of this administration mode, and to suggest the issues that need to be investigated in greater depth.