The Conundrum in Smart City Governance: Interoperability and Compatibility in an Ever-Growing Ecosystem of Digital Twins advances a rigorous critique of contemporary smart urbanism by exposing the structural fragmentation underpinning digital governance infrastructures in modern cities. Rather than celebrating smart cities as seamless technological achievements, the article demonstrates that the proliferation of isolated digital systems, proprietary platforms and incompatible data architectures has produced a fractured urban ecosystem incapable of achieving genuine interoperability. The authors argue that the accelerating deployment of City Digital Twins (CDTs)—real-time digital representations of urban systems—simultaneously intensifies and reveals the contradictions embedded within contemporary urban governance. Crucially, the article distinguishes between two competing integration paradigms: system integration, which consolidates existing tools into unified applications, and semantic integration, which employs ontologies and knowledge graphs to generate interoperable, context-rich data environments. This distinction constitutes the paper’s principal theoretical intervention because it reframes interoperability not merely as a technical challenge, but as a governance problem situated within broader political, institutional and socio-technical realities. Through comparative analysis of projects such as the Herrenberg Digital Twin in Germany, the Cambridge City-Level Digital Twin, and the semantic architecture of the World Avatar initiative, the paper demonstrates how knowledge graphs and semantic web technologies possess greater capacity to transcend institutional silos, enable cross-domain data sharing and support evidence-based planning processes. Particularly compelling is the argument that technological systems must become a “fourth dimension” of sustainability alongside economic, social and environmental concerns, thereby acknowledging the profound influence of digital infrastructures on urban life. Nevertheless, the article avoids technological determinism by emphasising unresolved tensions surrounding privacy, governance accountability, data monopolisation and citizen distrust. The authors conclude that future smart cities cannot rely upon one-size-fits-all technological solutions; instead, city administrations must proactively co-create flexible, participatory and interoperable digital ecosystems sensitive to local contexts and democratic needs. Ultimately, the article positions semantic digital twins not as purely computational instruments, but as evolving socio-technical assemblages capable of reshaping the epistemological foundations of urban governance itself.