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Relationships between groundwater and lake ecology are often overlooked, but they may be strong, particularly in seepage lakes. As a result, the nature and degree of groundwater effects on lakes are usually neglected. In this study interactions among rainfall, groundwater and surface water and their limnological effects were traced seasonally for two years of changing rainfall in a Spanish flowthrough, seepage lake complex. Cumulative rainfall dictated recharge of groundwater with delays of nine months. Groundwater discharge, in turn, increased surface discharge downstream. Mediated by the geographical setting of lakes, both fluxes impinged on lake water renewal time, but effects of the latter on limnological variables were much stronger at the district scale than at the single lake scale. These water-renewal effects included the following: decreasing salinity, total phosphorus concentration and phytoplankton biomass and increasing water transparency and total nitrogen concentration as water renewal shortened, the nitrogen effect arising because of nitrate-rich water entering the lakes as groundwater levels rose. This complex response of a Mediterranean lake district to water availability may also be expected in cold temperate lakes as climate change effects become stronger. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)