Paradigms based upon physical and geochemical bottom-up processes or trophic cascade/top down theory have been developed to explain heterogeneity of freshwater zooplankton, but these paradigms taken alone seem unable to encompass the full range of zooplankton variability and have led to controversy. The goal of the study is to test the hypothesis that both abiotic and biotic environmental factors, and spatial structuring, explain simultaneously the large-scale spatial heterogeneity of freshwater zooplankton in Québec lakes. Partial Canonical Correspondence Analysis (Partial CCA) was used to partition the variance of zooplankton species abundances into independent components: a) non-spatial environmental factors (physics, chemistry, morphometry, phytoplankton and fish communities), b) spatial component of environmental influence, c) pure spatial factors (geographic coordinates), and d) undetermined. Our study shows that pure and spatially-structured abiotic and biotic environmental factors (a+b) explain 48% of the variation of zooplankton within Québec lakes. Our study supports the multiple driving forces hypothesis and shows that the control model of the zooplankton structure within Québec lakes includes both abiotic factors (mainly related to the water chemistry gradients) and biotic bottom-up (phytoplankton) and top-down (fish) factors. Across our large geographic scale, the abiotic factors, especially those related to water chemistry, are the main environmental processes explaining zooplankton community structure variability within Québec. Pure spatial factors (c) have small and nonsignificant contribution (8%) to zooplankton variation. The large amount of unexplained variation (d: 44%) suggests that other external factors, operating at local scales and not taken into account in this study, can exert influence on lake zooplankton structure.