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The water balance, with large seasonal and annual water level fluctuations, has a critical influence on the nitrogen and phosphorus dynamics of shallow lakes in the semi-arid climate zone. We constructed seasonal water and nutrient budgets for two connected shallow lakes, Lakes Mogan and Eymir, located in Central Anatolia, Turkey. The study period covered 20 years with alternations between dry and wet years as well as restoration efforts including sewage effluent diversion and biomanipulations in Lake Eymir. Both lakes experienced a 1-2 m water level drop during a drought period and a subsequent increase during the wet period, with seasonal water level fluctuations of 0.60 to 0.70 m. During wet years with high water levels, small seasonal differences were observed with a nutrient peak in spring caused by external loading and nutrient loss via retention during summer. During years with low water levels, nutrient concentrations increased due to internal and external loading, exacerbated by evaporative water loss. In Lake Eymir, a shift to eutrophic conditions with turbid water occurred under low water level conditions and consequent internal loading of P from the sediment, causing high nutrient concentrations in summer. Our results indicate a threat of lakes drying out in the semi-arid climate zone if evaporation increases and precipitation decreases as anticipated from the global climate change predictions. In addition, our results show the influence of the water balance on the eutrophication of shallow lakes in the Mediterranean climate zone and highlight the ultimate consequences for lake management. (C) 2016 Elsevier B.V. All rights reserved.