Phytoremediation using floating treatment wetlands (FTWs) is an emerging nature-based solution for freshwater restoration. However, the potential to design these systems by manipulating macrophyte community composition to provide multiple ecosystem services remains unexplored. Using a tank experiment, we simulated aquatic environments impacted by multiple pollutants and employed a comparative ecological approach to design emergent macrophyte communities using the trait of plant stature (plant height) to structure communities. Ecosystem functions were quantified, and a threshold-based method used to compute an ecosystem multifunctionality index that was weighted based on three different management-driven restoration objectives: equal importance, phytoremediation, and regulation and cultural services. Across all restoration scenarios, ecosystem multifunctionality was higher when community types performed more diverse functions. Small emergent plant communities outperformed all other community types due to their increased provision of both regulation and maintenance, cultural, and provisioning services. Conversely, large emergent communities that are more typical candidates for phytoremediation had the highest levels of multifunctionality only when function was lower. Arranging emergent macrophytes in mixed-statured communities led to intermediate or poorer performance both in terms of multifunctionality and specific functions, suggesting that diversity on the plant stature axis leads to negative plant interactions and represents a ‘worst of both worlds’ combination. Employing comparative ecology to generalise plant selection by stature demonstrates that large emergent macrophytes are more likely to better deliver provision-based services, while small emergent communities can provide additional benefits from cultural and regulatory services. Selecting macrophytes for FTWs employed in freshwater restoration by stature is a simple and widely applicable approach for designing plant communities with predictable outcomes in terms of (multiple) ecosystem service provision and highlights the need for environmental managers to closely align restoration objectives with potential community types.