We investigated the effect of withdrawal of nutrient rich hypolimnic waters on diel changes in water column physicochemical conditions, composition of pelagic communities and metabolic processes over a 5-day period. The study was done during stratification in the eutrophic Kortowskie Lake divided into a southern experimental part with removal of near-bottom water by a pipe directly to the outlet, and a northern control part unaffected by the pipe. Volumetric metabolic rates with depth were calculated in each basin using 6 daily vertical profiles of dissolved oxygen (DO). Results demonstrated that withdrawal of near bottom water increased hypolimnic water temperature by 1.3°C decreasing the strength of thermal stratification. This increased phytoplankton biomass and primary production in the metalimnion of the experimental part of the lake, which became dominated by Cyanobacteria, and more net autotrophic compared to the photic zone of the control site. Daily variability in gross primary production (GPP), ecosystem respiration (R), and net ecosystem production (NEP = GPP-R) of the photic zone and metalimnion indicates the highly dynamic physical (mixing and light) and biological (pools of phytoplankton and bacteria) conditions occurring in the photic layers. In the control part of the lake, a multiple regression analysis showed that vertical patterns in GPP and R depended on phytoplankton biomass and total nitrogen and NEP followed changes in particulate organic carbon. In the experimental part of the lake, vertical patterns in NEP were only significantly related to changes in temperature. But as the temperature was positively correlated with bacterial abundance, this was most likely the main driver of variation in NEP with depth (relationship between R and medium cell volume (MCV), bacterial biomass (BB), respectively: r=0.60; r=-0.63; n=15; p<0.05, Pearson's correlation). The strong effects of hypolimnic withdrawal on physico-chemical and biological conditions shown by our short-term study, suggest that this method weakens thermal stratification, enhancing nutrient inputs from hypolimnic waters causing elevated phytoplankton biomass and primary production in metalimnetic and epilimnetic layers shifting the overall metabolic balance of the water column toward net autotrophy. On the other hand, biodegradation processes in higher temperature and intensive sinking of organic matter to the sediment and then removing by pipe directly to the outflow, reduce significantly phytoplankton biomass in the hypolimnion of experimental part of the lake.