Quantification of the response of wetlands to environmental change and of climate change to wetland processes, is a pressing, but complex, issue. Findings of widely diverse investigations have to be generalised to identify the key issues and the gaps in knowledge. Two tools for generalisation, scaling and uncertainty analysis, were applied here to two case studies and act as stepping stones for analysis of key issues. The first case study is on methane emissions from wetland rice fields and the second is on the restoration of wet dune slacks. The type of problems encountered depends on the scale at which a process is studied. At the biogeochemical processes scale, knowledge on some key parameters, but especially on interactions between key parameters is limiting. At the vegetation scale, feedbacks between processes become especially important, whereas at even larger scales increasingly stringent approximations of interactions have to be made. Accumulating uncertainties at the landscape scale need careful evaluation. Apart from uncertainties in the approximations and their interactions, those introduced by spatial and temporal variability as well as by different data sources highly influence the accuracy of response estimates, while these last sources of uncertainty are neglected in many studies. Only by explicitly accounting for scaling effects and their resulting uncertainties, the interactions between wetlands and environment can be understood.