Rice (Oryza sativa L.) production in the United States is primarily concentrated in the Mississippi River Delta region of south-eastern Missouri, eastern Arkansas and Louisiana, and western Mississippi, and rice-based cropping systems are different from other row crops due to the flood-irrigation scheme used from about one month after planting to a few weeks prior to harvest. The frequent cycling between anaerobic and aerobic conditions can influence the rate of soil organic matter decomposition, which sequentially affects soil water-stable aggregation and carbon (C) and nitrogen (N) sequestration over time. Water-stable aggregation and C and N storage in agriculturally managed soil can also be affected by tillage practices, crop rotation, and fertilization treatments. Understanding agricultural practices that influence soil aggregation is crucial to developing management strategies that will increase soil C and N sequestration at regional and global scales. A study was conducted on a silt-loam soil (fine, smectitic, thermic, Typic Albaqualf) in the Mississippi River Delta region of eastern Arkansas to evaluate the long-term effects of rice-based crop rotations [with corn (Zea mays L.), soybean (Glycine max L.), and winter wheat (Triticum aestivum L.)], tillage [conventional tillage (T) and no-tillage (NT)], and soil depth (0- to 5-cm and 5- to 10-cm) after 10 years of consistent management on soil water-stable aggregation and C and N accumulation within five aggregate-size classes (0.25- to 0.5-mm, 0.5- to 1-mm, 1 to 2-mm, 2- to 4-mm, and > 4 mm). Results showed that the concentration of water-stable aggregates increased as aggregate-size class decreased. There was also a greater concentration of water-stable aggregates under NT at the 0- to 5-cm depth than any other tillage-depth treatment combination for all rotations. Furthermore, the C and N concentrations of equivalent aggregate-size classes were roughly 2.5 times greater in the 0- to 5-cm depth than the 5- to 10-cm depth in all aggregate-size classes sampled. Among cropping systems, rotations with increased frequencies of corn generally had a greater water-stable aggregate C and N content in comparison to other rotations. Soil aggregates play an important role in maintaining soil aeration, water infiltration, soil structural stability, and physical protection for soil organic matter storage, and finding soil management practices that maintain these physical properties of the soil is important in assuring the long-term sustainability of row crop agriculture.