Addressing challenges of water, energy and food security, nexus approaches towards resources management are being developed and starting to be implemented. However, the ecosystem perspective, essential for sustainable resources management, has been identified as a missing element within earlier nexus assessments. With regard to water they have mainly focused on the allocation to different sectors and users, while ecosystem services were rarely explicitly addressed. Existing aquatic ecosystem models are capable of quantifying a wide range of ecosystem services, but have thus far not been comprehensively used in a nexus context. Recent developments in aquatic ecosystem modelling approaches provide opportunities to achieve the sought integration of ecosystem services in the nexus approach. Therefore, we argue for a stronger role of aquatic ecosystem models in nexus assessments.