The data set contains the raw data used for the analysis in a study to the effect of guanotrophication on algae abundance in Lake Lesser Prespa Greece, as described in the research paper by Valentini et al. in PLOSONE. Lake Lesser Prespa in Greece is a vital breeding habitat for the Dalmatian and Great White Pelican. However, eutrophication processes are distressing the lake system and the outbreaks of cyanobacterial blooms during the warm months may pose a threat to aquatic organisms due to the presence of microcystins (MCs). In this study we hypothesize that nutrients (eutrophication), nutrient-rich pelican droppings (guanotrophication) and warming (climate change) can affect the algal growth and MCs production in the water layer of Lake Lesser Prespa.An experiment (bioassay) was set up where water of (three sites in) lake Lesser Prespa was incubated at two temperatures (20°C and 30°C). Five treatments were used at both temperatures to study the algal development on a short term: 1) control, 2) nitrogen addition, 3) phosphorus addition, 4) nitrogen+phosphorus addition 5) bird dropping addition.In this repository the following data are included:-Chlorophyl-a concentrations in the water (initial and end-concentrations and of additional validation experiment);-Several nutrient concentrations in the water (initial and end-concentrations);-Several nutrient concentrations in bird droppings of pelicans;-Microcystin concentrations in the water (end-concentrations).