Water level fluctuations are a global phenomenon creating temporary aquatic systems. Recent trends in climate and land use changes have led to their spatio-temporal expansion, meaning that temporary streams and lakes show longer periods of low water level or that currently permanent systems switch to a temporary regime. Drying and re-flooding often greatly affect redox-sensitive processes, such as the decomposition of organic material and phosphorus dynamics. Both are generally regarded as key ecosystem processes making them valuable indicators for functional ecosystem health. This work describes how preconditioning of leaf litter in dry systems reduced the leaf quality considering it a substrate for aquatic decomposer communities and as a result reduced leaf decomposition rates. In the sediments, even a single drying event was shown to result in the transformation of phosphorus components into more labile forms, which are accumulated in the near-surface sediment layer, and therefore raise the potential of pulsed P release under reducing conditions.