Dissolved organic carbon (DOC) concentrations in many freshwater ecosystems of the northern hemisphere have increased in recent decades due to additional terrestrial inputs. This phenomenon, known as brownification, can strongly alter the physical, chemical, and biological traits of aquatic ecosystems. Extreme rainfall can also cause sudden brownification, known as blackwater events in rivers, while longer term effects on lakes are unknown. Here, we investigated the resilience of a small, temperate, shallow lake to a strong natural flooding-induced brownification event in 2011-2012. From initial DOC and total phosphorus (TP) concentrations of ~12 and 0.04 mg L -1 , respectively, the lake rapidly reached peak DOC and TP concentrations of 60 and 0.35 mg L -1 , respectively. By the following year, water levels had returned close to initial values, yet two additional years of monitoring (until summer 2015) and a more recent sample in spring 2019 showed that the lake did not fully return to its pre-brownification state. Instead, DOC and TP concentrations plateaued at concentrations respectively 1.5-fold and twofold greater than pre-brownification values within less than two years and remained at these concentrations in spring 2019. During this initial recovery period the lake exhibited a decline of phytoplankton and a partial recovery of summer periphyton biomass and production, albeit a full return to pre-brownification values was not recorded in either case. DOC and TP concentrations were positively correlated to phytoplankton biomass and negatively to periphyton. As increases in phytoplankton production outpaced decreasing periphyton production, the net result of this brownification event has been an increase in whole-lake areal summertime primary production. This incomplete resilience to a flooding-induced brownification event implies consequences for several ecological and biogeochemical functions of shallow lakes that warrant further investigation and might contribute to the gradual increase of freshwater DOC concentrations in the northern hemisphere.