This investigation tested the hypothesis that the alternate wet and dry (AWD) water regime would increase soil microbial biomass carbon (MBC), microbial biomass nitrogen (MBN) and microbial count. Variations in MBC, MBN and grain yield could be due to varietal differences in a derived savanna.  Experiments (both pot and field ones) were conducted at the Federal University of Agriculture, Abeokuta (Latitude 7° 12’ to 7° 20’ N and Longitude 3° 20’ to 3° 28’ E), Nigeria in 2015. In both trials, the treatments consisted of water regimes (continuous flooding [control] and AWD imposed on lowland rice varieties [NERICA^® L-19] and Ofada [local check]) at the vegetative growth stage in three cycles. The design in both trials was a completely randomised and randomised complete block design for the pot and field experiments respectively, with three replicates. In the screen house, MBC and MBN were significantly higher in AWD than in continuously flooded soil, especially at the beginning of the AWD cycles. This could have caused nutrient pulses to sustain the improved performance of lowland rice under AWD. A converse pattern was observed in the field in the third cycle. Ofada rice had a significantly higher microbial count and MBC (cycle 1) than NERICA L-19, however, a converse pattern was observed in MBC (cycles 2 and 3) and MBN (cycle 1). Composition of their rhizodeposition and timing of cycles could explain the observed varietal differences in MBC and MBN.