ABSTRACT The global impacts of agricultural land conversion on soil erosion and pollution, particularly in tobacco cultivation areas, are well-recognized as significant contributors to soil degradation. These areas are identified as hotspots for environmental concerns due to practices that lead to increased erosion and pollution. From this perspective, this case of study explores fine sediment samples from two areas with tobacco cultivation under different tillage systems and seasonal variations, transport into a headwater, and evaluates, on a local scale: (1) the impact of tillage systems on the geochemical signature of sediments; (2) if whether crop seasonality affects these sediment geochemical signatures. The Conventional Ridge Tillage (CRT) system involves extensive soil exposure and machinery for soil management, while the Mulch Ridge Tillage (MRT) system prioritizes soil conservation and relies on herbicides for weed control. The analytical methodology used to assess the sample element characteristics was Energy Dispersive X-ray Fluorescence (EDXRF). It was applied on the twenty fine sediments (ten of harvest and ten of inter-harvest season of tobacco) to quantitatively assess their inorganic composition. Additionally, Pearson correlation analysis, Hierarchical Cluster Analysis (HCA), and Principal Component Analysis (PCA) were applied on the EDXRF data to highlight the similarities and, thus, providing information to assess the complex data clustering patterns. As a result, the sediment compositions from the two studied soil systems are not similar. The PCA showed that the CRT sediments are characterized by the P, S, K, Ca, and Mn content, presenting a geochemical signature related to manure and fertilizer compared to the MRT, which is correlated with Al, Ti, Fe, Cu, and Zn contents, exhibiting a geochemical signature characterized by the natural soil composition. Therefore, the sediment geochemical signatures might be affected by two phases in the study area: a) tillage system characteristics and b) seasonal soil erosion. These findings underscore the importance of managing soil nutrients to mitigate soil pollution and nutrient exportation to aquatic systems. Moreover, the results emphasize the recommendations for sustainable agricultural practices in tobacco-growing areas to protect environmental quality.