In an abandoned shrimp pond, the spatial variability of the height of nipa (Nypa fruticans Wurmb.) plants 5 years after their planting was evaluated to elucidate the determining factors for height. Soil properties were evaluated in 20 points in an area of 0.48 ha. Physical (e.g., hardness, water content) and chemical (e.g., pH and EC) properties were determined using surface soil samples collected at each point. Nipa height was moderately variable, showing a CV value of 31.2%. Soil conditions were considered to affect nipa height; therefore, principal component analysis (PCA) was conducted to elucidate the relationships among soil properties. As a result, three factors were extracted. PC1 correlated positively with relative ground level and Eh, and negatively with moisture. Because these properties were closely related to topography, PC1 was referred to as the topography factor. PC3 showed the second important contribution, a high K content contributed to a large nipa height. Multivariate analysis was also performed to examine the spatial property of nipa height (H), and as a result, the following equation was obtained: H = 423.94 - 0.39 x PC1 - 0.57 x PC3 (r²=0.53). Results of this study indicate that 53% of nipa height variation was explained by soil properties, which is larger than the nipa height variation explained solely by topography (23%). Site-specific management to regulate soil properties could be a practical strategy for nipa plantation.