Weed management is the major challenge to the success of boro rice (rice grown during Dec–Jan to May–Jun, also known as summer rice) in Southern Asia. Herbicide seems to be a cost effective and strategic tool from an agronomic view point to control weeds; however, herbicide application can potentially interfere with soil enzyme activity and microbial biomass carbon (MBC). A field study was conducted in 2012/13 and 2013/14 to evaluate the performance of sole and combined application of different pre-emergence herbicides in comparison to manual weeding in boro rice. Lowest weed density, biomass and highest weed control efficiency (~83%) were recorded with the pyrazosulfuron ethyl, causing higher grain yield (6.7 Mg ha−1 in 2012/13 and 4.5 Mg ha−1 in 2013/14) than treatments with chlorimuron + metsulfuron-methyl, bensulfuron methyl + pretilachlor, butachlor fb 2,4D, butachlor and cono-weeder. Among, the herbicidal treatments butachlor caused lower grain yield and higher weed density and biomass when compared to the others. Although grain yield was highest in weed-free treatments but net returns and (B:C) benefit cost ratio was highest for pyrazosulfuron ethyl due to high cost of hand weeding. After 15 days of herbicide application, lowest microbial biomass carbon was recorded with bensulfuron methyl + pretilachlor, whereas lower values of dehydrogenase and fluorescein diacetate activities were observed with the application of chlorimuron + metsulfuron-methyl at 15 days after herbicide application. Our results suggest that pyrazosulfuron ethyl is one broad-spectrum and economically effective herbicide for controlling weeds as an alternative to labour consuming hand weeding in boro rice cultivation.