The restoration of degraded ecosystems and landscapes is challenging, because returning to the original state is often socio-economically unfeasible. A novel approach is to construct new ecosystems to improve the functioning of degraded landscapes. However, the development of novel ecosystems is largely driven by the pre-construction hydrogeophysical and ecological conditions of the soil. In Lake Markermeer, a deteriorating freshwater lake in the Netherlands, a large archipelago is currently being constructed to boost the ecological functioning of the lake. Hence, islands – with wetlands and with more elevated and dryer areas – have been created to sustain biodiversity and key biogeochemical functions such as nutrient cycling. The islands are constructed from lake-bottom sediments. To study how two potentially important drivers, water level and bioturbation, affect soil characteristics in a novel wetland ecosystem, we experimentally tested the effects of water level (-30, -10 and 5 cm), and bioturbation by earthworms (Lumbricus rubellus) and Tubifex spp. in a microcosm experiment. We demonstrate that a high water level prevents soil subsidence, soil crack formation and carbon dioxide (CO2) emissions, and affects nitrogen cycling. In dryer soils, the presence of earthworms strongly increases CO2 emissions next to reducing soil crack formation, while Tubifex spp. in wetter soils hardly affect soil characteristics. Our findings highlight the important roles of both water level and bioturbation for the functioning of novel soils, which likely affects vegetation development in novel ecosystems. This knowledge can be used to aid the construction and nature development of novel wetlands.