1. The Mancha Hú meda Biosphere Reserve includes approximately 50 lakes, most of them shallow and temporary (lagunas).2. Despite their international importance, numerous impacts affect them, including pollution in lagunas located near villages and the partial or total desiccation of most sites due to river channelization and groundwater over-exploitation.3. Restoration attempts over a period of years failed because they aimed to improve living conditions for only unrepresentative indicator taxa and neglected the temporal dynamics of aquatic systems.4. Key recommendations are discussed for restoration, based on functional analysis: i) Restoring and/or preserving the original hydroperiod (including drought) and the diversity of water input; ii) protecting the structure and function of sediments, considering nutrient availability to assess water quality; iii) categorizing the environments in terms of the dominant primary producers; iv) complementing estimates of production by considering its fate and form of consumption; and v) identifying key events triggering the main patterns of ecosystem organization (either episodical or periodical, abiotic or biotic).