Sensors and biosensors as well as biochemical responses (biomarkers) in ecosystems owing to environmental stress provide us with signals (environmental signalling) of a potential damage in the environment. These responses are perceived in this early stage, but in ecosystems, the eventual damage can be prevented. Once ecosystem damage has occurred, the remedial action processes for recovery could be expensive and pose certain logistical problems. Prevention of ecosystem deterioration is always better than curing. Ideally, “early warning signals” in ecosystems using sensing systems and biochemical responses (biomarkers) would not only tell us the initial levels of damage, but these signals will provide us as well with answers to develop control strategies and precautionary measures with respect to the water framework directive. To understand the complexity of the structure of populations and processes behind the health of populations, communities and ecosystems, we have to direct our efforts to promote rapid and cost-effective new emerging parameters of ecological health. New emerging parameters are biochemical effect (biomarker) related parameters in the field of immunotoxicity and endocrine disruption. Environmental effects such as genotoxicity and clastogenicity were detected in organisms from various “hot spots”. Vital fluorescence tests are one means that allow us to unmask adverse events (i.e., genetic alterations in field-collected animals or in situ-exposed organisms) by a caging technique. New emerging ecosystem health parameters are closely linked to biomarkers of organisms measured in monitored areas. One problem is always to find the relevant interpretation and risk assessment tools for the environment.