Herbicides have become an indispensable part of crop production as the most economical and assured means of weed control. However, herbicides have been affecting the various components of agroecosystem and natural ecosystems owing to its persistence nature in soil and adverse effects on flora and fauna. Weed flora shift, development of herbicide resistance and accumulation of herbicide residues are the major areas of concern in the agroecosystem. Conversion of minor weeds viz. Commelina benghalensis and Lagascea mollis (less than 4.0/m2 at harvest) in 1999 to major weeds (density to 13 to 20/m2) in 2007 owing to continuous application of butachlor was observed in finger millet-groundnut cropping sequence [1]. Microbial activity and population dynamics of microorganisms have been affected due to continuous application of herbicides. Soil treated with butachlor at the rate of 0, 0.4, 0.8 and 1.6 mg/kg soil, showed significantly lower Azotobacter count and the extent of decline in the population increased with increase in butachlor dose [2]. Herbicide resistance is a worldwide phenomenon and numbers of resistant biotypes of weeds are increasing at an alarming rate. Development of resistant biotypes of common weed genera viz. Amarantus (42 biotypes), Chenopodium (25 biotypes), Lolium (21 biotypes), Avena (15 biotypes), Senecio (12 biotypes) etc., have been a serious ecological concern [3]. Use of herbicides in natural ecosystem like aquatic ecosystem have short term effects like reduction in oxygen, increase in carbon dioxide, decrease in the pH, change in the nutrient status of the water and in plant communities, with a consequent alteration of habitat for the fauna and finally complete habitat destruction in the long term [4]. Integrating the mechanical and cultural management practices encompassing herbicide rotation, crop rotation, adoption of HRC’s along with use of safe herbicides, bioherbicides, alleloherbicides are the most appropriate options for mitigating the negative effects of herbicide use in different ecosystems.