Europe's ambitious new nature restoration legislation aims to restore ecosystems to enhance nature conservation, biodiversity, and climate change mitigation efforts. Resilient ecosystems with high biodiversity demonstrate reciprocal relationships between physical processes and biotic components, which act as "ecosystem engineers" and are considered Nature-based Solutions. However, little is known about the presence and environmental functions of ecosystem engineers prior to their eradication or decline in heavily human-modified European landscapes, a knowledge gap that significantly hampers restoration initiatives. Promising new restoration approaches like rewilding or stage 0 approaches will struggle to succeed without a comprehensive understanding of the original, natural state of these ecosystems and their human modification. Here, we aim at collecting studies using e.g. sedimentary ancient DNA (sedaDNA) - but also other new and exciting palaeoecological proxies or the modelling of natural processes - as tools for analyzing sediments with the goal to reveal how biota and humans are influencing past ecosystem dynamics and vice versa. We invite studies that reconstruct past ecosystems, their drivers and feedbacks, including the reconstruction of human-modified and natural states, or the co-evolution of physical and biotic-driven processes over a Holocene time-scale. Additionally, we encourage work that considers how these studies can support practitioners to enable the implementation of Europe's largest natural restoration scheme.