This dataset provides ANUGA hydrodynamic modeling results and input run-scripts for the Atchafalaya basin in the Mississippi River Delta in southern Louisiana, USA, during three windows of time corresponding to the Delta-X and Pre-Delta-X field campaigns in fall 2016, spring 2021, and fall 2021. ANUGA is a 2D depth-integrated hydrodynamic model which uses the Finite Volume Method (FVM) to numerically solve the shallow water momentum and continuity equations for fluid flow in broad-scale geophysical systems. Each iteration of the model was extensively calibrated using a database of in-situ and remotely-sensed observations, including about 54 water level gauges, numerous water surface profiles collected by AirSWOT or lidar, and water level change measurements derived from UAVSAR. The model was forced using observational data collected from NOAA and USGS, and the model mesh was specifically designed to capture channel-island connectivity using high-resolution Planet Labs imagery spanning over a decade. In total, over a month of simulation outputs are included in this dataset, covering different seasons and hydrological conditions in the Atchafalaya and Wax Lake Delta systems. These model outputs can be leveraged with other Delta-X datasets to provide contextual information about water levels or flow velocities at different times or locations within the Atchafalaya basin, and the model codes provided can be used to simulate additional time periods for further analysis in this region. Model outputs are presented in NetCDF (.nc) format and run-scripts are in Python (.py) or contained in compressed (*.zip) file format.