The rain falls more frequently on the high moors of Chinchón and Villaconejos and reaches the wetland by runoff, through the gullies of the gypsum cliffs, or by underground infiltration favored by the structure of the land in the form of stepped terraces. Direct recharge through precipitation in the form of rain is scarce at the bottom of the fertile plain, where the San Juan lagoon sits, but it serves to recover the optimal wetland habitat in a short time and reactivates wildlife in the marsh refuge. Water losses are mainly due to underground seepage and solar evaporation, accentuated in the hot summer months, when most of the birds migrate to other wetlands to seek food and shelter.
The resident birds in the Laguna de San Juan Fauna Refuge and the nearby environment of the fertile plain and gypsum cliffs are the western marsh harrier, royal blue eagle, eagle owl, purple swamp, common kestrel, black wheatear, common coot, gray heron, falcon basking, kingfisher, red duck, great crested grebe and little grebe. The wintering bird species in the wetland are the great cormorant, marsh bunting, cattle egret, shoveler, European pochard and tufted duck. And the birds present in the summer season in the lagoon and the surrounding steppe mountains are bee-eaters, little bitterns, sand martins, common reed warblers, great gray warblers and purple herons.
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