Pharmaceutical compounds are emerging contaminants of concern, which can elicit sub-lethal effects to non-target organisms and present a human health risk via the contamination of drinking water. Exacerbated by their increased consumption and poor removal rates from wastewater treatment plants, pharmaceutical compounds have been classified as pseudo-persistent in the aquatic environment, and their monitoring is imperative. It is now widely accepted that conventional methods of monitoring are inadequate, and the implementation of novel holistic approaches which provide biological data, identify mechanisms of toxicity as well as predict pollution are essential to safeguard the environment from pollutants including pharmaceuticals. Employing the sentinel species Daphnia magna and integrating holistic techniques such as metabolomics and biochemical markers, the molecular responses to individual pharmaceuticals or complex mixtures was explored in the concept of daphnids acting as the “canary in the coal mine” within the aquatic environment. Specifically, the effects of oestrogens, antibiotics, environmentally relevant drugs (anticonvulsants, NSAIDs, lipid regulators, antidiabetics) and a pharmaceutical mixture were assessed through acute, chronic and in some instances transgenerational exposures, endpoints ranged from phenotypic i.e. mortality, enzyme, reproduction, size to molecular i.e enzyme activity and metabolomics. Exposure to oestrogens revealed impaired enzyme activity, distinct differences in the polar metabolic profile, as well as decreased protein content and size of daphnids, while antibiotic exposure showed altered enzyme activity, the upregulation of hydrophilic metabolites following acute exposure, and a trend to downregulate the metabolites of central metabolism following transgenerational exposure. This contrasts with the environmentally relevant drugs which mostly upregulated the intermediates of central metabolism and polar metabolites. To assess the synergistic effect of the pharmaceuticals, daphnids were exposed to a mixture as well as environmental samples, which revealed many changes in enzyme activities and the metabolome.