Use of pesticides continues to be indiscriminate, and birds are one of the worst affected non-targeted organisms. Information on the ill effects of pesticides on birds far from desired in India. Despite the presence of a wide variety and number of birds, there is exceedingly little data on organochlorine pesticide (OCP) residues in colonial nesting birds in sanctuaries of India. A total of 76 individuals belonging to 14 species of birds found dead between March 2008 and March 2010 were analyzed for pesticide residues in various tissues. Of all the OCPs analyzed, concentration of HCH was found to be the highest. Magnitude of contamination varied widely among species. Accumulation pattern of OCPs in colonial nesting birds was in the order ∑HCH > ∑endosulfan > ∑DDT > heptachlor epoxide > dieldrin. Pesticides, namely p,p-DDE and β-HCH contributed most towards the total OCPs. Concentrations of DDT and its metabolites, HCH and isomers, dieldrin, and heptachlor epoxide were lower than the concentrations reported for various species of birds elsewhere in India. Although the sanctuaries presently studied have official boundaries, physical demarcations are missing and there are no proper earthen dykes particularly in Vedanthangal and Koonthankulam Bird Sanctuaries. During monsoon, runoff not only floods the Sanctuaries but also the cultivated areas nearby. Run off brings in residues of pesticides and fertilizers from the agricultural lands into the sanctuaries. Although OCP results in this study were below threshold limits, it may be noted that the long duration exposure even to low levels of pesticides could create a significant impact at population level. Hence, earthen dykes need to be built to avoid agricultural runoff entering the Sanctuary and also help to hold sufficient amount of water for breeding birds.