This study was conducted at the Experimental Farm of rice department, Sakha Agricultural Research Station, Egypt during 2015 and 2016 summer seasons to investigate the effect of recommended doses from Stomp (pendimethalin 50% EC) and Rainbow (penoxsulam 2.5% OD) herbicides on weed control, microbial activities and rice productivity under drill-seeded rice cultivation. Total bacterial count, N₂-fixing bacteria, N₂-fixing cyanobacteria, nitrifiers and sulfate-reducing bacteria were counted at different periods of crop growth. Dry weight of Echinochloa crus-galli, Echinochloa colona, Ammania baccifera and total weeds were measured at 45 and 60 DAS. Paddy rice dry weight at 45 and 60 DAS, number of panicles, panicle weight and grain yield were determined. The results revealed that total bacterial count, nitrogen-fixing bacteria, native N₂- fixing cyanobacteria and nitrifying bacteria were increased with penoxsulam application, while sulphate reducers were decreased in both seasons compared with application of pendimethalin and the untreated control. Penoxsulam application significantly decreased dry weight of Echinochloa crus-galli, Echinochloa colona and total weeds. While increased rice dry weight, number of panicles/m², panicle weight and grain yield of rice in the two growing seasons.