The monitoring of organic compounds in aquatic matrices poses challenges due to its complexity and time-intensive nature. To address these challenges, we introduce a novel approach utilizing a dual-channel mono (1D) and comprehensive two-dimensional (2D) gas chromatography coupled with time-of-flight mass spectrometry (GC × GC–TOFMS) system, integrated with a robotic pretreatment platform, for online monitoring of both volatile organic compounds (VOCs) and semivolatile organic compounds (SVOCs) in water matrices. Employing the robotic platform, we establish a suite of online liquid–liquid extraction (LLE) pretreatment processes for water samples, marking the first instance of such procedures. Leveraging the automatic headspace (HS) module, dual robotic preparations of HS and LLE are sequentially executed to extract VOCs and SVOCs from water matrices. The GC × GC–TOFMS system is distinguished by its dual-channel analytical column configuration, facilitating sequential analysis of VOCs in GC–TOFMS mode and SVOCs in GC × GC–TOFMS mode. Quantitative detection of 55 target VOCs and 104 SVOCs is achieved in a water sample using the instrument system. Our method demonstrates excellent correlation coefficients ranging from 0.990 to 1.000, method detection limits ranging from 0.08 to 4.78 μg·L−1, relative standard deviations below 19.3%, and recovery rates ranging from 50.0% to 124.0%. To validate the online monitoring capabilities of our system, we assess target SVOCs at three different concentration levels over a 3-day period. Most compounds exhibit recovery rates ranging from 70.0% to 130.0%. Furthermore, we apply our method to analyze a real water sample, successfully identifying over 100 target and nontarget VOCs/SVOCs, including alcohols, aldehydes, ketones, acids, esters, and phenols. These results highlight the efficacy of the proposed analysis system, capable of conducting two distinct analyses in automatic sequence, thereby enhancing the efficiency and accuracy of organic compound analysis in water matrices.