Utilising multiple lines of evidence for palaeoenvironmental reconstruction improves our understanding of the past landscapes in which human populations interacted with other species. Illuminating such processes is key for a nuanced understanding of fundamental transitions in human history, such as the shift from hunting and gathering to farming, which move beyond simple deterministic interpretations of climate-driven innovation. Avifaunal remains can provide detailed indications of complex multi-species interactions at the local scale. They allow us to infer relationships between human and non-human animals, but also to reconstruct their niche, because many bird species are sensitive to specific ecological conditions and will often relocate and change their breeding patterns. In this paper, we illustrate how novel evidence that waterfowl reproduced at Levantine wetlands, which we obtained through biomolecular archaeology, as well as modern ornithological data, can reveal conditions of wetlands that are conducive for breeding waterfowl. By understanding the interplay between wetland cover cycles and waterfowl ecology, we argue that human modifications to the environment would have promoted wetland productivity inviting waterfowl to remain year-round. Within this landscape of "mutual ecologies", the feedback resulting from the agency of all species is involved in the construction of the human niche.