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We describe the long-term (1981&#8722;2008) dynamics of several physico-chemical and biological variables and how their changes may have influenced zooplankton structure in Lake Maggiore (Italy). Data was available for the 1981&#8722;1992 and 1995&#8722;2008 periods. Standardized time-series for temperature and total phosphorus (TP), chlorophyll-a, phytoplankton density (cel m^&#8722;3), and cell size (&#181;m³), as well as zooplankton structure (Copepoda, Cladocera, and Rotifera density, ind m^&#8722;3) were smoothed using penalized B-splines and analyzed using Functional Principal Components (FPCs) to assess their dominant modes of variation. The first four FPCs explained 55% of 1981&#8722;1992 and 65% of 1995&#8722;2008 overall variation. Results showed that temperature fluctuated during the study period, particularly during 1988&#8722;1992 with a general tendency to increase. TP showed a declining trend with some reversions in the pattern observed in the years 1992, 1999, and 2000. Phytoplankton estimators and chlorophyll-a concentration showed a variable trend along the study period. Zooplankton groups also had a variable trend along the study period with a general increase in density of large carnivorous (mainly <i>Bythotrephes longimanus</i>) and a decrease of large herbivorous (mainly <i>Daphnia</i>), and a similar increase in the ratio of raptorial to microphagous rotifers. Our results suggest that the lake experienced a strong trophic change associated with oligotrophication, followed by pronounced climate-induced changes during the latter period. TP concentration was strongly associated with changes in abundance of some zooplankton taxa.