Manure enhances soil fertility and crop yield; however, an optimum rate of manure application is important to avoid any negative impacts to soils and the environment. This study was conducted to assess the long-term impacts of manure and inorganic fertilizer rates on soil organic carbon (SOC), total nitrogen (TN), water stable aggregate (WSA), pH, and electrical conductivity (EC) under corn (Zea mays L.)-soybean (Glycine max L.) rotation at Beresford (established in 2003) and Brookings (established in 2008), South Dakota (SD). Study treatments included low (LM), medium (MM) and high (HM) manure, medium (MF) and high (HF) inorganic fertilizer, and control (CK). Soil samples were extracted from four replicates at 0- to 10-cm, 10- to 20-cm, 20- to 30-cm and 30- to 40-cm depths from either site in 2015. Results showed that manure application maintained the soil pH at 0 to 10 cm depth; whereas, inorganic fertilizer decreased it compared to the control treatment at either site. The highest SOC concentrations at 0- to 10-cm depth were observed under HM (38.3 g kg(-1)) as compared to that under MM (30.9 g kg(-1)), LM (27.6 g kg(-1)), MF application (24.0 g kg(-1)), HF (25.8 g kg(-1)) and CK (23.3 g kg(-1)). Furthermore, HM treatment significantly increased SOC for each depth increment from 0- to 40-cm compared to the inorganic fertilizer at either site. A similar trend was observed for the TN but differences were not always significant. On an average, manure increased the EC (1.56 dS m(-1)) by 2.2 times compared to that of fertilizer (0.71 dS m(-1)) for 0- to 10-cm depth. Similarly, manure significantly increased WSA by 7.2 and 5.6% compared to that of fertilizer at 0- to 10-cm depth for Brookings and Beresford, respectively. Data from this study concluded that the long-term annual application of manure improved selected soil properties compared to that of inorganic fertilizer.