The presented study investigates the dynamics of DOC concentrations in headwater peatbog areas with respect to the extreme rainfall-runoff (R-R) events hydrometeorological catchment preconditions (23 variables in total). The main data sources were automatic devices for monitoring of groundwater level, discharges and rainfalls providing data in 10 min steps installed in the Vydra River catchment and one automatic water sampler ISCO in sub-catchment of the Rokytka River basin in the Šumava (Bohemian Forest) National Park. The study period was 2018–2021, in which 18 R-R events were analysed. Data of DOC variability and catchment conditions were analysed using Spearman’s correlation coefficient, Principal Component Analysis and DOC/Q hysteresis loops. Changes in groundwater level and discharges had the greatest influence on DOC concentrations. Higher mean and maximum DOC were measured during events after a longer period without an extreme R-R event. The greater lag time of maximum DOC after peak flow and the higher mean DOC during the event were primarily due to hydrometeorological preconditions of the catchment. The highest DOC was in autumn after the previous summer period with low discharges and low groundwater levels. DOC was also positively correlated with air and water temperatures.