Monitoring data from Flemish rivers and channels. The data contains phytoplankton counts of Flemish lakes and pools. Water bodies were monthly sampled during the growing season of a one-year period, from a bridge of the shore using a bucket. Each time, a 250ml subsample fixed using 125µl alcalic lugol, 6.25ml borax buffered formaldehyde (35%) and 250µm sodiumthiosulfaat (5 %).Samples were kept dark and cool until microscopic analysis, which was executed according to the European CEN-standard (EN 15204, 2006). In this method, a known volume of the sample was concentrated in a cuvet, after which different phytoplankton taxa were identified along a transect using an inverted microscope (Wild M40). When to much detritus was present, samples were coloured using Bengal red, to enable recognizing cells. For each sample, at least 250 individuals were counted, which was used to calculated to number of individuals per ml. Colonies were counted as one individual.