Thanks to open science initiatives, thousands of standardised datasets on Earth System compartments are now available on the web. In particular, we have widely used ISO 19115 to encode spatiotemporal aspects of Earth System observations. However, this standard does not specify the multiple dimensions of observations, including the features of interest, the observable properties, and the provenance. As a result, researchers interested in Earth System multi-disciplinary studies may miss meaningful datasets when querying independently domain-specific data portals. We propose a new Dataset Discovery System based on SOSA and DCAT ontologies, as well as the User-Centric Metadata Model (UCMM), to integrate dataset metadata from multiple data portals, each representing an Earth System compartment. The descriptive UCMM metadata model is exploited simultaneously to address semantic and structural heterogeneities and to build a descriptive Knowledge Graph explaining how retrieved datasets are semantically related to the user’s search. We introduce the implementation of two Earth System Dataset Discovery use cases. The experiments and user uptake demonstrate the benefits of the Dataset Discovery System in multi-disciplinary Earth System studies.