Unlike most of the other basins in the State, groundwater divides do not always correspond with surface-water divides in the Neponset, Weymouth, and Weir River basins. One prominent example of this occurs along parts of the southern boundary of the Neponset basin, where groundwater flows north from the Taunton River basin into the East Branch Neponset River basin.

Stratified sand and gravel aquifers are the principal source of groundwater in the Neponset, Weymouth, and Weir River basins. These aquifers underlie about one half of the area of the basins and, where they are thick and near surface-water bodies, can yield more than 300 gal/min to wells. Some of the thickest deposits, more than 150 ft thick, underlie parts of the Neponset River valley. The head of the Neponset has been designated a sole-source aquifer by the USEPA (U.S. Environmental Protection Agency). In addition, bedrock and glacial till throughout most of the basins can usually provide a few gallons per minute of water to wells.