Water column sampling for nutrients, chlorophyll-a and bacteria was carried out at different time-scales covering 12 hours and one month; ten replicated samples were taken for estimating the stochastic variability. Two sampling stations were established on the north coast of Crete (eastern Mediterranean), one in Heraklion harbour and a second one at an exposed coastal area. All variables measured were significantly higher in the port. Only chlorophyll-a showed an increasing coefficient of variation with increasing time scale at both sampling sites, whereas the other variables showed different patterns between the two sites.