Repeated and long term application of same herbicides forms bound residues in soil and becomes point source of pollution over a period of time and harms the soil microorganisms. Among the different herbicides, the atrazine and pendimethalin is widely and repeatedly used molecule in maize and sunflower cultivation for weed control, respectively. Hence the present study was undertaken to investigate the bound residue of the applied herbicides in soil under long term fertilized condition with varied nutrient sources since 1909 in North-Western agro-climatic zone of Tamil Nadu under the semi-arid tropic region of India.  Soil samples were collected at the time of maize and sunflower harvest and analysed for the bound fraction of atrazine and pendimethalin compounds respectively. The results showed that the repeated application of these herbicides at recommended dose formed a considerable amount of non-extractable bound residues in soil. While the bound fraction of parent atrazine was found below detectable limit, pendimethalin was at a quantifiable level in the soil irrespective of fertilization sources. However the bound form of atrazine metabolites, namely Des ethyl Deisopropyl atrazine (DEDIA) and Hydroxy atrazine (HA) was extracted from the maize cultivated soil. Bound forms of HA (4.34%) and DEDIA (3.43%) and pendimethalin (3.14%)to the applied quantity were witnessed at a higher amount in control plot than the fertilized plots. The omission of any one major nutrient recorded elevated DEDIA bound form than the HA fraction. The non-extractable bound residues of both the herbicides were detected at different proportions according to the herbicide nature, sources of fertilization and the crops cultivated in the soil. The fraction of bound form of atrazine metabolites was detected at higher level than the pendimethalin in soil. The present study revealed that the bound residues of atrazine, its metabolites and pendimethalin can be mineralized into the soil solution and bio-augmented over a period of time under the conditions of repeated application. Hence the remobilization of bound residues of these herbicides must be considered while gauging the environmental hazard and effect on non-target organisms.