Flooded paddy soil ecosystems in the tropics support the cultivation of the majority of the world's leading crop, rice, and nitrogen (N) availability in the paddy-soil rooting zone limits rice production more than any other nutritional factor. Yet, little is known about the dynamic response of paddy soil to N-fertiliser application, in terms of horizontal and vertical patchiness in N distribution and transformation. Here, we present a microscale analysis of the profile of ammonium (NH4(+)) and nitrate (NO3(-)), nitrification, oxygen (O2water and O2soil), and pH (pHwater and pHsoil) in paddy soils, collected from two representative rice-production areas in subtropical China. NH4(+) and NO3(-) exhibited dramatic spatiotemporal profiles within N patches on the microscale. We show that pHsoil became constant at 1.0-3.5 mm depth, and O2soil became undetectable at 1.7-4.0 mm. Fertiliser application significantly increased pH, and decreased O2, within N patches. Path analysis showed that the factors governing nitrification scaled in the order: pHwater > pHsoil > NH4(+) > O2water > NO3(-) > O2soil. We discuss the soil properties that decide the degree of nutrient patchiness within them and argue that such knowledge is critical to intelligent appraisals of nutrient-use efficiencies in the field.