Human activity is affecting and transforming the natural environment, changing the ecosystem mosaic and natural biogeochemical processes in urban-industrial landscapes. Among the anthropogenic ecosystems, there are many present features of Novel Ecosystems (NE), e.g., the de novo created habitats on post-mineral excavation sites. The biological nature of the functional mechanisms of Novel Ecosystems is mostly unknown. In natural and semi-natural ecosystems, biodiversity is considered as the primary element influencing ecosystem processes and functioning. The preliminary studies conducted on post-mineral excavation sites have shown that, in poor oligotrophic habitats, the species composition of the assembled vascular plants is non-analogous, distinctive, and not found in natural and semi-natural habitats. This paper aims to present the gaps between scientific identification of the biological mechanisms driving ecosystem processes and functioning (including the expanding areas of Novel Ecosystems created de novo). Among the identified gaps, the following issues should be listed. The detailed identification and understanding of the processes and biodiversity-dependent functioning of Novel Ecosystems is crucial for proper environmental management, particularly when facing the challenges of ecological constraints and of global change. The ecology of Novel Ecosystems is a social and economic issue because of the relationships with densely populated urban-industrial areas.