Understanding how the hydrological regime in relation to sediment type interferes with ecosystem development is important when wetlands are created with soft muddy material. Especially when plants are used as ecological engineers to promote crest stability and soil formation. We carried out a two-year mesocosm experiment with sediments derived from the Dutch lake Markermeer to identify the effects of the hydrological regime and sediment type on ecosystem functioning in terms of nutrient availability. We measured plant productivity, plant nutrient stoichiometry, and concentrations of N, P, and K in shoots and roots of Phragmites australis and Rumex maritimus and monitored how the clay-rich sediment from lake Markermeer changed into a wetland soil. Plants grown on Markermeer sediments tend to be N limited when periodically inundated and P limited when not inundated at all. The P availability was determined by the hydrological regime, while the N availability was determined by both the hydrological regime and the sediment type. Ecosystem development on created wetlands can be manipulated by adequate management of the hydrological regime, as plant species respond differently to changes in nutrient availability. This should be considered in eco-engineering projects where plants are used as ecological engineers to fasten ecosystem development on wetlands that are to be created from clay-rich material.