While it is well-accepted that predation plays a key role in shaping both size structure and species composition in natural ecosystems, fine-scale variation in predation risk within ecosystems has been largely neglected. The objective of this study was to use normalised size spectra (NSS) to investigate whether small-scale spatial variation in predation risk (by fish) can modulate zooplankton community structure at the within-lake level in a small temperate lake.We tested the difference in the NSS between two hydrologically well-connected basins of a lake exhibiting contrasting thermal regimes. The first is a well-mixed shallow basin (max. depth 2.5 m) that is inaccessible to brook charr (Salvelinus fontinalis) during summer because the temperature is too warm. The second is a deeper basin (max. depth 18 m) offering a thermal refuge during summer because of lake stratification. As a consequence of these differences in fish accessibility, the fishless basin should contain larger and more abundant zooplankters, inducing a change in NSS slope and height.Our results showed that both the zooplankton size structure and taxonomic composition were distinct in the two basins, with a higher proportion of small individuals and a higher abundance of zooplankton in the shallow basin compared to the deep one. Furthermore, following cooling of the epilimnion in late summer, the zooplankton communities of both basins exhibited a clear shift in size structure and species composition: in autumn, there were smaller individuals and larger proportions of Bosminidae and Daphniidae compared to colonial rotifers than in summer. These results suggest a potential effect of the change in the spatial distribution of brook charr which feed preferentially on large individuals, reducing the average body size of the zooplankton community.Our results show that predation risk by fish can induce a spatial and temporal variation in zooplankton community structure within small temperate lake ecosystems exhibiting contrasted thermal regimes. Other potential predators also influenced the zooplankton community structure, creating a complex interplay that has to be taken into account to disentangle ecological processes and predict their future changes.