A generalized model for well hydraulics in confined aquifers is presented. The lattice Boltzmann method (LBM)-based altered-velocity model is used to simulate well hydraulics in homogeneous and heterogeneous confined aquifers for different pumping conditions. LBM is applied to simulate well hydraulics in two different configurations of heterogeneous aquifer, where (1) a circular disk of material or (2) an infinite linear strip of material is embedded in a matrix of differing hydraulic properties. The effect of hydrogeologic boundaries on drawdown curve in confined aquifers is simulated using LBM. The LBM is further applied to simulate drawdown during harmonic pumping well test. The LBM data in lattice units are scaled to physical units using non-dimensional discharge rate and diffusion length. The results from LBM were found to be sensitive to the relaxation parameter and the RMS error for drawdown was found to be less than 1% for later time. This work will verify the potential of LBM to simulate well hydraulics in homogeneous and heterogeneous confined aquifers for constant, step, and harmonic pumping.