To reduce external nutrient loading by the greatest nutrient transporter to Lake Balaton, the Kis-Balaton Water Protection System commenced operation in 1985. Cyanobacterial blooms (Cylindrospermopsis raciborskii, Aphanizomenon sp. and Anabaena sp.) cause nitrogen loading via nitrogen fixation, which can exceed the total external N-load to the reservoir during the summer. Nitrogen fixation of phytoplankton in the system in 2009 was measured using the 15 N-isotope technique. The light dependence of fixation was described by an exponential saturated curve which was then used to calculate daily nitrogen fixation. The total amount of nitrogen fixed during summer months (July-August) exceeded 170 tons for the 21 km 2 of open water area, which was more than three times higher than the external load by inflows. Total nitrogen: total phosphorus mass ratios (2.5−11.5) favoured the development of a N 2 -fixing cyanobacterial bloom, the contribution of which to the total algae biomass varied between 50 and 90%. The estimated primary production of phytoplankton was used to calculate the contribution of nitrogen fixation (0.01−28%) to algae nitrogen demand. Nitrogen fixing cyanobacteria were found to play a key role in addressing the nitrogen demand of phytoplankton.