Suspended sediment (SS) continues a century-long decline in the Lower Mississippi and Atchafalaya Rivers, United States. In this study, we use the WRTDSplus model to estimate concentrations and loads for total, fine (<0.0625 millimeter (mm)), and coarse (≥0.0625 mm) SS for 11 sites. This extension of the Weighted Regressions on Time, Discharge, and Season (WRTDS) model allows a fourth explanatory variable in the model formulation. We incorporated hysteresis terms for most models based on a residual analysis, which allowed for the identification of decreased flushing over time at some sites. Total, fine, and coarse SS concentrations and loads decreased at all sites over two trend periods (water years (WY) 1992–2021 and WY 2012–2021). Declines were largely due to changes in fine SS (mud and silt) but decreases in coarse SS (sands) were also widespread. On average, recent declines are more severe in the Lower Mississippi River below the Old River Control Complex (ORCC, −3.7 mg per liter per year (mg/L/yr)) compared to the Atchafalaya River (−2.0 mg/L/yr), although there is longitudinal variability within each river. The reach below the ORCC is a net SS sink, leading to complex temporal changes for the sites in this area. Streamflows (low, moderate, and high) have increased over these periods, with the last decade being particularly wet. Increasing streamflow and decreasing SS, with little evidence of amelioration, may influence spillway operations during floods, sediment diversion construction and operation, coastal restoration efforts, and aquatic health.