The monitoring of phytoplankton is an important component of water quality assessment in artificial and natural lakes. The evolution of eutrophication in an urban man-made lake (Palácio de Cristal, Porto, Portugal) was followed after remediation measures were applied. Nutrients as well as the phytoplankton community were monitored and the results compared with those of a previous study. Sampling was done in four sites of the lake so as to assess the efficiency of NO3 removal by the phytoplankton. The data of this study showed a reduction in NO3 levels in the underground source water, which caused a reduction in the phytoplankton abundance. The nitrate removal by the phytoplankton in the lake was on average 51% and was much lower compared with previous studies of the same lake. The dominant cyanobacteria species were Pseudanabaena spp., probably due to the low water residence time. Monitoring of potentially toxic cyanobacteria, by molecular methods based on the use of toxin gene primers, will be an efficient early warning method. This will allow the application of corrective management measures before an intense toxic bloom occurs.