Water quality monitoring using fish and crayfish as bio-indicators requires an understanding of the state of pollution of waters, choice of bio-indicators, physiological and behavioral endpoints of fish and crayfish, and principles of the methodology and their potential applications. Here, we discuss telemetry, acoustic monitoring, vision-based monitoring, measures of ventilatory activity, electrocardiography, and fiber-optic plethysmography. Assessment of water quality must be based, not only on physicochemical characteristics of the current environment as determined by chemical analyses, but also on observations of the physiology and behavior of its inhabitants. Real-time biomonitoring is suggested as the most reliable method, since it incorporates living organisms into the system to serve as biosensors. The potential application of the methods discussed includes use at water treatment plants and water supply stations for prevention of hazardous toxicological events, and, for aquaculture, in ponds, lakes, and aquariums for monitoring growth, population size, and behavior traits.