Long‐term irrigated rice (Oryza sativa L.) cultivation is an important yet unstudied source of soil variation in tropical lowland rice fields. A field study was conducted to quantify spatial soil variability and to analyze correlations among soil properties at different spatial scales. Soil samples from the 0‐ to 20‐cm depth were collected from adjacent rice fields consisting of Typic Tropaquepts and Typic Tropaqualfs. Structural variogram analysis and factorial kriging (FKA) were used to describe the coregionalization of 14 soil properties. Coregionalization was described by a model comprising (i) a nugget effect, (ii) a spherical model with a range of 12 m, and (iii) a Gaussian model with a range of 36 m. Correlations among soil properties varied depending on spatial scale. Short‐range soil variation was caused by irrigation and land leveling, but results were not consistent for both fields. Similar autovariograms and high correlations between depth to the Cg horizon and extractable K in the Gaussian structure (ρ2uv = −0.95 to −0.99) revealed a strong influence of weathering of volcanic tuff on long‐range trends in K. Electrical conductivity (EC), Na, and B were spatially trended and correlated with depth to the Cg horizon (ρ2uv = 0.59–0.97) in the Gaussian structure. Subsurface water flow through cracks above an impermeable layer and surface water flow along the gentle field slope were sources of long‐range variation in EC, Na, and B caused by irrigation. The FKA provides quantitative measures of complex spatial process results and offers new ways for generating hypotheses about the phenomenon itself.