279-290Time series data of monthly averages, over three stations, for counts of zooplankton groups and species, and some environmental factors (water temperature, salinity and chlorophyll a) were collected from the Eastern Harbor of Alexandria, during the period of 48 months, from October 1999 to November 2003. The spectral density graphics with frequency indicated that inspite of the presence of several peaks for different variables the only significant peak, at 95% confidence limit, was found in case of water temperature. The results of Fourier analysis show that the most common periods that are relatively important and affecting the movement of the time-series of environmental and the biological variables are 12, 9 and 6 months. The 12 months was corresponding to seasonal changes, while periods less than 12 months were due to local changes depending on the hydrological exchange between the Eastern Harbor and the open Mediterranean coastal waters in front of the study area. The time lags of the occurrence of the maxima of each two variables at the important cycles with periods 12, 9 and 6 months were calculated to express the response time of the different groups flourishing relative to the occurrence of the effecting environmental factors. The cluster and correlation analyses of the different variables have also been done to show most correlated ones. The results indicated that the annual cycle is the most important one in most cases. The multiple regression equations between the zooplankton counts and the environmental variables showed the important controlling factor in the different species and groups of zooplankton