Freshwater ecosystems are subject to numerous natural and anthropogenic pressures. The main objective of this research was to investigate the processes and molecular responses of several key components of freshwater ecosystems while exposed to multiple stressors. To this end, laboratory experiments were conducted with i) caddisflies and macrophytes exposed to microplastics, pharmaceuticals and endocrine disruptors, and ii) biofilms exposed to drought and a mixture of emerging contaminants. A robust method was developed for simultaneous characterisation of stressors and monitoring the corresponding molecular responses of organisms, allowing the detection of emerging contaminants (pharmaceuticals, endocrine disrupting compounds and microplastics), metabolites and proteins from a single tissue sample. By analyzing metabolic and total protein variations, the experiment on caddisflies and macrophytes provides valuable insights into adverse effects of microplastics on aquatic organisms and compares the effects of microplastics with those of pharmaceuticals and endocrine disruptors. The biofilm experiment shows a dynamic interaction between the microbial community and its environment during exposure to desiccation and emerging contaminants. Desiccation stress shapes the microbial community, which in turn, under the influence of emerging contaminants, modulates chemical composition of the environment.