Landscape scale assessment of temporal variations in soil organic carbon (SOC) contents and soil pH and the implications for long-term agricultural sustainability was determined using legacy datasets collected over two periods separated by 20 years: the 1990s and 2010s. Soil data on SOC and pH were categorized according to the prevailing land types (based on inundation as highland (HL), medium highland (MHL), and medium lowland (MLL)), and physiographic types (i.e., Himalayan Piedmont plain, Tista Floodplain and Barind tract/Terrace) to determine which variable or combination of variables was more influential in spatial and temporal changes of these properties. SOC contents in the physiographic types were generally found to be low, varying between 8 to 12 g/kg. While, SOC contents were significantly higher in MHL and MLL compared with HL that experienced less inundation. The change in SOC contents over 20 years was significant with a 14.5% increase of SOC. There was a greater influence of land type compared with physiography on SOC contents over time. Inundation land types and associated cropping intensity were considered likely to influence SOC of soils under rice-based cropping systems. Furthermore, the levels of soil pH decreased by 0.5 units over 20 years with an approximately 50% increase in soils within a pH category of 4.6–5.5. The majority of soil pH results shift from slightly acidic to strongly acidic in the intervening 20-year period between samplings. Soil acidification is potentially a combination of inefficient and excess use of ammonium-based fertilizers with higher application rates and low input from residues. We conclude that acidification may continue with more intensive land use. However, trends in SOC contents over time under certain combinations of physiography and land type either increased slightly or showed a significant loss and in the latter, specifically, the role of land management is not clear. The legacy datasets would be useful for monitoring spatial and temporal soil quality trends at a regional scale, but has limited capacity to capture field level variations in soil properties as data on smallholder cropping practice and management were not collected. Therefore, future research examining the role of management in SOC and pH dynamics at the field-scale would guide the use of fertilizers, crop residue management, and amelioration of acidic soil, to improve the sustainability of rice-based cropping systems in Bangladesh.