AbstractAround the 1930s, the zooplankton (and benthos) of the Nile delta lakes, and Lake Borullus in particular, had a mixed, eutrophic facies, with marine and mesohaline elements dominant for about eight months per year, and freshwater species taking over during the four months of the Nile flood. After the Aswan dam became operational, this regime changed: a steady supply of agricultural drainage water of Nilotic origin consistently freshened the delta. Thus, except in the immediate vicinity of their outlet to the sea, the lakes became almost fresh. Only during the rare and short‐lived (one‐three weeks) occasions when Aswan closes in winter, marine water is sucked in, and along with it, a saline fauna temporarily becomes re‐established in the east and centre of lake Borullus, and presumably of the other delta lakes as well. This marine fauna remained the same over 70+ years of observations. The freshwater component, in contrast, partly nilotic, partly mediterranean, changed deeply over time. First, the fraction of species from temporary waters disappeared, as well as (among copepods and cladocerans) all large‐bodied species. Several cladocerans and copepods with a euro‐mediterranean range appeared and diluted the pre‐existing Afrotropical fauna. The abundance of small cladocerans and, especially, rotifers increased by a factor ten or more. This latter change is believed to reflect two pressures. In a first phase, a re‐arrangement of the lake's fish fauna (a top down force) occurred. Freshwater fish replaced marine diadromic species, and their predation pressure on the zooplankton preferentially removed large‐bodied prey. In a second phase, increased agricultural drainage caused eutrophication (a bottom‐up force) and larger filtrators (cladocerans, some copepods) began to be replaced by small filtrators (rotifers). (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)