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Herbicides (HBs) are an integral part of modern agricultural practice globally as one of the most suitable methods for chemical weed control. Hence, they may inadvertently damage crops through similar mechanisms well-functioning at weeds. Tolerance to three categories of treatments (tribenuron-methyl, 2,4 D and their combination), and the impact of the mode of application (pre-treatment of seeds or spraying on plants) was assessed through morphometric analysis (total plant length, root length, stem length, lengths of the first three leaves, relative water content-RWC), and pigment content analysis for some wheat (Triticum aestivum L.) cultivars in use in Albania. Results speak of a cultivar specific tolerance to each HB category, discriminating “Dajti” as the most resistant cultivar, and suggesting that the stress imposed to plants by the combination of HBs can produce significant differences in pigment content. The mode of treatment, on the other side showed that glyphosate pre-treatment of seeds led to inhibition of germination, and plants germinated from seed pre-treatment with in 2,4-D displayed significant modification of plant morphology, and germination rate, and had limited impact on RWC. On contrary, few statistically significant changes in morphometric traits and pigments content were evidenced when plants were treated with 2,4-D or glyphosate after the germination. In conclusion, the combination of HBs produced significant changes in plant pigments content compared to the impact of each HB alone, and the pre-treatment of seeds lead either to inhibition or delayed germination. Based on the above we recommend avoiding these practices, and suggest further exploration of alternative HB combinations and modes of treatment before large scale applications.