The term “population synchrony” refers to the phenomenon of synchronous fluctuations of populations. The strength of this phenomenon may indicate the nature of the synchronizing mechanisms. In this study, we evaluated the relative importance of the Moran effect and dispersal on the levels of population synchrony in a zooplankton assemblage. We monitored the density of 36 taxa (27 genera, Bdelloidea, cyclopoid nauplii, calanoid nauplii, cyclopoid copepodites, calanoid copepodites and four broad taxonomic groups) at 7 sites through 19 months (from May 2004 through November 2009). For each taxon, we estimated the regional levels of synchrony as the mean Spearman correlation coefficient for all pairwise combinations of sites. These values were significant for 33 of the 36 taxa analyzed. Variations in synchrony were uncorrelated with hydrological or geographical distances. Environmental synchrony was unrelated to distance. The low relationship between synchrony (both environmental and population) and hydrological distance indicates the importance of the Moran effect. Nevertheless, climatic effects were not the main synchronizing mechanism. We suggest that damming was the main synchronizing force in this system.