The community composition and metabolism of Mediterranean temporary lakes are sensitive to meteorology, determining the length of the flooded period and water depth. We studied the biological communities and metabolism of Laguna de Talayuelas, a Mediterranean temporary lake selected as a model to disentangle key ecological processes. The development and activity of hydrophytes were determined by hydrology. Water depth favoured differential development of emerged-floating versus submerged species. Rooted macrophytes, especially Ranunculus, extracted nutrients from the sediments, making them bioavailable for phytoplankton after senescence. During the studied period the lake showed three functional phases. The first period, with low water depth, was governed by autotrophic processes and coincided with the development of submerged macrophytes. These accounted for most lake’s productivity, and a highly diverse community was maintained. A second phase occurred by late spring, coinciding with a sudden increase of the water depth after strong rainfalls; then submerged macrophytes decayed and decomposed, and respiration increased. The lake had a net heterotrophic behaviour and biodiversity decreased. During the third period, in summer, nutrients released from macrophytes decomposition favoured phytoplankton blooms. The system turned to net autotrophy but now based on phytoplankton photosynthesis. Floating macrophytes developed, though the benthic component maintained net heterotrophy.