Hydrophobic organic contaminants (HOCs) are conventionally screened by matching electron ionization (EI) mass spectra acquired using gas chromatography-mass spectrometry (GC-MS) to reference spectra. However, extensive in-source fragmentation hampers de novo structure elucidation of novel substances that are absent from EI databases. To address this problem, a new method based on GC-atmospheric pressure chemical ionization (APCI) coupled to ion mobility-high resolution mass spectrometry (IM-HRMS) was developed for simultaneous target, suspect, and nontarget screening of HOCs. Of 102 target chemicals, 85.3% produced (quasi-)molecular ions as base peaks, while 71.6% displayed method detection limits lower than those of GC-EI-low resolution MS. The optimized method was applied to standard reference sediment and sediments from the Baltic Sea, an Arctic shelf, and a Norwegian lake. In total, we quantified 56 target chemicals with concentrations ranging from 4.86 pg g-1 to 124 ng g-1 dry weight. Further, using a combination of full scan mass spectrum, retention time, collision cross section (CCS), and fragmentation spectrum, a total of 54 suspects were identified at Confidence Level (CL) 2. Among the remaining features, 169 were prioritized using a halogen-selective CCS cutoff (100 Å2 + 20% mass), leading to annotation of 54 substances (CL ≤ 3). Notably, a suite of fluorotelomer thiols, disulfides, and alkyl sulfones were identified in sediment (CL 1-2) for the first time. Overall, this work demonstrates the potential of GC-APCI-IM-HRMS as a next-generation technique for resolving complex HOC mixtures in environmental samples through exploitation of molecular ions.