An effective framework for groundwater modelling is a precursor for sustainable management of regional water resources. Owing to the coexistence of contrasting hydrogeological units, modelling of groundwater flow through multi-layered fractured aquifers such as the granitic aquifers found in the Deccan region of India, requires an accurate estimation of hydraulic parameters and delineation of preferential flow-paths. There are several approaches towards this goal. This study compares seven methods by evaluating their abilities to reconstruct the hydraulic parameter distributions of a synthetic two-dimensional multi-layered aquifer analogue whose construction is based on pre-existing field data. The methods studied are (1) a homogeneous parameter model; (2) a single-hole equivalent model that provides an average of local-scale estimates; (3) a geostatistical single-hole model that involves kriging of the single-hole local-scale estimates; (4) a uniformly placed pilot-point model; (5) the sequential successive linear estimator (SSLE) algorithm; (6) a geostatistical-guided pilot-point model; and (7) a new approach that involves a pilot-point model guided by the results of the SSLE algorithm. The results of the inversions are compared visually using tomograms and by a statistical analysis of the time-drawdown datasets obtained from validation wells that were not used for calibrating the models. The uniform pilot-point model performed significantly better than the other methods. The SSLE algorithm recovered the fracture connectivity pattern with significant fidelity. Using the SSLE algorithm as a guide improved the parameter estimation at the cost of the fracture connectivity pattern. © 2021, Springer-Verlag GmbH Germany, part of Springer Nature.