A hierarchical sampling was performed in order to give a picture of the horizontal distribution of cyanobacterial colonies. It showed how the importance of different scales in distance changed during the summer bloom of Gloeotrichia echinulata in the moderately eutrophic and stratified Lake Erken in southeastern Sweden. G. echinulata colonies occurred in patches at a distance of ∼1000 m and the variance at smaller scales was low. For colony content of phosphorus, chlorophyll a and size, however, the largest variances were found at the 20 m (and error) scale if the variances between dates are not taken into account. It was concluded that in order to estimate the lake population of cyanobacterial colonies properly these variances must be considered when deciding the sampling program.