Smoking is not only a main contributing cause in several diseases with implications in human health, but as the most popular habit with global consumption, it has severe implications and impact on the ecosystem, something that remains uncontrolled. Smoking leaves behind cigarette filter butts, which take up to fifteen years to decompose and can concentrate a great number of toxic compounds. These compounds leach out into the aqueous environment, polluting surface waters. Pollution assessment is based on the detection of chemicals and pollutants in the environment to estimate quality; however, such measurements are merely descriptive and provide, to their limit of detection, a report of the panel of pollutants present without any mechanistic information for their action. Therefore, water chemistry methods cannot predict the appearance of specific pollutants early. This is the reason why in the latest years' environmental risk assessment and monitoring are moving towards effect-based methods and novel approach methodologies as more sensitive tools for risk assessment. These approaches use biological systems and molecular information as new metrics for monitoring. Focusing on the freshwater ecosystem, the water flea is a sentinel organism used extensively in ecotoxicology. Combining phenotypic and holistic approaches, we screened for the molecular effects of a cigarette and an e-cigarette on daphnids following the analysis of filter extracts to assess their chemical composition. We identified perturbations in the physiology and metabolism of daphnids with feeding, enzyme activities, mortality and survival, and metabolic perturbations. Aiming to elevate the water flea as an equivalent to “a canary in the coal mine”, we intend to identify the presence of cigarette pollutants in the environment in actual river samples.