Biological and environmental sciences are, more than ever, becoming highly dependent on technological and multidisciplinary approaches that warrant advanced analytical capabilities. Microfluidic Lab-on-a-Chip technologies are perhaps one the most groundbreaking offshoots of bioengineering, enabling design of an entirely new generation of bioanalytical instrumentation. They represent a unique approach to combine micro-scale engineering and physics with specific biological questions, providing technological advances that allow for fundamentally new capabilities in the spatio-temporal analysis of molecules, cells, tissues and even small metazoan organisms. While these miniaturized analytical technologies experience an explosive growth worldwide, with a substantial promise of a direct impact on biosciences, it seems that Lab-on-a-Chip systems have so far escaped the attention of aquatic ecotoxicologists. In this review, potential applications of the currently existing and emerging chip-based technologies for aquatic ecotoxicology and water quality monitoring are highlighted. We also offer suggestions on how aquatic ecotoxicology can benefit from adoption of microfluidic Lab-on-a-Chip devices for accelerated bioanalysis.