Summary Pollution is a global issue at the frontier between ecology, environmental science, management, engineering and policy. Legislation requires experiments to determine how much contamination an ecosystem can absorb before there are structural or functional changes. Yet, existing methods cannot realistically simulate regimes of chemical disturbance and determine impacts to assemblages in ecosystems. This is because they lack ecologically relevant species and biotic interactions, are logistically difficult to set up and lack environmentally relevant regimes of chemical and abiotic disturbance that organisms experience in polluted areas. We solved these long‐standing environmental, logistical, experimental and ecological problems by developing a programmable dosing system. This dosing system simulates, in situ, regimes of chemical disturbance to assemblages by manipulating the concentration, duration, timing and frequency of pollutants to which they are exposed. Experiments with priority pollutants (the metal copper and the biocide chlorpyrifos) and mussel assemblages revealed consistent plumes of contamination within patches of mussel. Mussels at the sources of experimental plumes of copper created by the dosing system, accumulated 670% more copper in their tissues compared to mussels 0·5–50 m away. In addition, when mussels were exposed to increasing concentrations of copper, there was a concomitant increase in the amount of copper in the tissues of mussels. Combining the dosing system with an established hierarchy of ecotoxicological assays revealed mussel assemblages exposed to copper and/or chlorpyrifos had 40–70% fewer worms, whilst chlorpyrifos alone caused an 81% reduction in the number of amphipods and caused mussels to filter 48% fewer particles from the water. Combinations of copper and/or chlorpyrifos had no effects on the abundance of crabs, the respiratory functions of assemblages or the viability of molluscan haemocytes. As global contamination accelerates, we discuss how this technological advance will enable a diverse array of ecologists, mangers and policy‐makers to understand and reduce pollution.