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This study presents the first systematic investigation into the influence of spectral enhancement techniques on the segmentation accuracy of specific soil and vegetation marks associated with palaeochannels. These marks are often subtle and can be seasonally obscured by vegetation dynamics and soil variability. Spectral enhancement methods, such as spectral indices and statistical aggregations, are routinely applied to improve their visual discriminability and interpretability. Despite recent progress in automated detection workflows, no prior research has rigorously quantified the effects of these enhancement techniques on the performance of deep learning–based segmentation models. This gap at the intersection of remote sensing and AI-driven analysis is critical, as addressing it is essential for improving the accuracy, efficiency, and scalability of subsurface feature detection across large and heterogeneous landscapes. In this study, two state-of-the-art deep learning architectures, U-Net and YOLOv8, were trained and tested to assess the influence of these spectral transformations on model performance, using Sentinel-2 imagery acquired across three seasonal windows. Across all experiments, spectral enhancement techniques led to clear improvements in segmentation accuracy compared with raw multispectral inputs. The multi-temporal Median Visualisation (MV) composite provided the most stable performance overall, achieving mean IoU values of 0.22 ± 0.02 in April, 0.07 ± 0.03 in August, and 0.19 ± 0.03 in November for U-Net, outperforming the full 12-band Sentinel-2 stack, which reached only 0.04, 0.02, and 0.03 in the same periods. FCC and VBB also performed competitively, e.g., FCC reached 0.21 ± 0.02 (April) and VBB 0.18 ± 0.03 (April), showing that compact three-band enhancements consistently exceed the segmentation quality obtained from using all spectral bands. Performance varied with environmental conditions, with April yielding the highest accuracy, while August remained challenging across all methods. These results highlight the importance of seasonally informed spectral preprocessing and establish an empirical benchmark for integrating enhancement techniques into AI-based archaeological and geomorphological prospection workflows.