Abstract Microbial processes such as mineralization, nitrification and denitrification regulate nitrogen dynamics in the soil. The last two processes may produce nitrous oxide (N2O). In this work N2O fluxes were quantified at four moments of the rice cycle, sowing, tillering, panicle initiation and maturity, in two sites that differed mainly in their soil organic matter (OM) content, Salto (higher OM) and Treinta y Tres. Potential net N mineralization, ammonium oxidation and denitrification as well as the most probable numbers (MPN) of ammonia oxidizers and denitrifiers were determined.