Sindh is in the lower reaches of the Indus River; it is most vulnerable to a variety of upstream water development challenges. The aim of this research was to determine aquifer characteristics in the command area of Tando Allahyar-II distributary within the culmination of underground water potential. The hydraulic properties of the aquifer as well as the susceptibility of the formation to tedious extraction and saltwater upcoming were recognized. Three pumping tests were performed at head, middle, and tail reaches along the selected distributary. The drawdowns were measured at head reach (5.1667 h), at middle reach (6.0 h), and at tail reach (19.667 h) of the selected distributary by performing the pumping tests. Groundwater levels were lower at the tail reach compared to those at the head and middle reaches, likely due to a higher concentration of tubewells in the lower reach. The head and middle reaches showed higher groundwater levels, possibly due to constant head conditions promoting infiltration and recharge. The pumping test versus drawdown analysis revealed that the tubewells should be run with 7-h (on) and 4-h (off) operation. Further, the tubewells at all reaches (head, middle, and tail) should be closed for a minimum of 4 h between operations. This strategy would allow safe groundwater extraction, maintain water quality, and prevent water table depletion in the study area. The hydrodynamic and hydro-salinity behaviors were scrutinized in PWMIN 5.3 (version) by means of the MODFLOW mode. The results were estimated to compare the calibration and validation simulation outcomes using measured data. The model was successfully calibrated, and the root mean square (RMS) value of the head tubewell varied between 0.024 and 0.108, whereas it speckled between 0.0166 and 0.0349 for the middle tubewell and between 0.0659 and 0.0069 for the tail tubewell. The RMS values for hydrodynamic behavior for the head, middle, and tail reaches were less than 10%. These values represent a suitable match between the observed and simulated heads when a water table depletion of 1 to 2 m was observed due to extreme pumping. However, the average relative error values, for all validated procedures, were less than 10%.