Abstract: Short-chain chlorinated paraffins (SCCPs) represent a class of typical persistent organic pollutants whose trace detection in aquatic matrices is essential for ecological security and human health risk assessment. This article systematically examines recent advances in SCCPs pollution status, sample pretreatment techniques, and instrumental analytical methodologies in aquatic matrices. It provides a comparative evaluation of six pretreatment approaches—including solid-phase extraction and liquid-liquid extraction—highlighting their respective advantages and limitations. This article assesses two main analytical approaches: traditional targeted analysis and emerging non-targeted screening, examining the applicability and constraints of chromatography-mass spectrometry techniques in targeted approaches, while also exploring the potential of high-resolution mass spectrometry for identifying unknown transformation products. Finally, future research directions are proposed, emphasizing innovation in pretreatment materials and refinement of detection techniques. This will help establish effective method and a scientific basis for trace SCCPs monitoring and risk management in aquatic matrices.