Due to the shifting course of the Brahmaputra River, the fluvial landforms of the Brahmaputra Valley of Assam, India, are prone to changes in landform and land use. For sustainable soil management under such conditions, it is crucial to have information about soil physicochemical and biological properties for different land uses. Therefore, the present study was conducted to investigate the soil physicochemical properties and soil microbial population across five major land uses under different landforms, such as paddy fields, banana systems, and arecanut cultivations in the alluvial plains; and rubber plantations and sal forests in the uplands, with varying slope gradients and soil depths (0–25 cm and 25–50 cm) in the lower Brahmaputra Valley. The results of the analysis of variance revealed that the effects of different landforms and land uses were found to be statistically significant on very labile soil organic carbon (VLSOC), available K, B, Fe, Mn, Zn, and Cu, and soil moisture content across two different soil depths. Paddy cultivated systems recorded the highest (1.23%) soil organic carbon (SOC), but these levels were statistically at par with other land use scenarios except for banana systems; whereas, forests and rubber plantations showed the highest VLSOC (0.38% and 0.34%, respectively,) and were significantly different from other land use scenarios. All soil microbial populations (bacteria, fungi, and actinomycetes) studied varied significantly in different land uses across varying soil depths. Perennial land uses under arecanut, rubber, and forest cultivations showed significantly higher microbial populations than paddy and banana systems. The principal component analysis (PCA) identified SOC, VLSOC, Cu, K, B, P, and the bacteria count as the major soil quality parameters of the study area. The results showed that landforms, land use, and management practices collectively affect soil properties. Therefore, soil management choices should take into consideration the landforms and land use for maintaining soil health and its sustainability.