The zebra mussel is an important aquatic pest that causes great damage to freshwater-dependent industries, due to biofouling. The main goal of the project discussed here is to develop improved solutions to control this species. Three approaches have been explored in an attempt to design innovative application strategies for existing biocides: (i) encapsulation of toxins; (ii) combination of toxins; (iii) investigation of the seasonal variation of the species' tolerance to toxins. In this paper, the principles behind these approaches and the major results on each topic are presented. The benefits of adopting a chemical product engineering approach in conducting this project are also discussed.