Abstract Do observation wells in fractured porous aquifers measure water head in the fracture network, water head in the matrix, or some combination of both? This question necessarily arises when calibrating dual‐continuum hydrogeological models against on‐field data. One can assume that observation wells measure fracture water head, because matrix permeability is negligible compared to fracture permeability. Nevertheless, this reasoning is invalid for wells poorly‐connected to the fractures. Yet, the possibility of such a poor connection at given depths has never been implemented in a physics‐based manner when comparing matrix and fracture water heads simulated by dual‐continuum models to on‐field data. To fill this knowledge gap, a physically based, easy to calibrate, open‐source postprocessing tool, POWeR‐FADS (Program for Observation Well Representation in Fractured Aquifer Dual‐continuum Simulations), available at https://github.com/BJeannot1/POWeR-FADS , has been developed. It introduces as parameters well geometry and the altitude of lowest interception of the fractures by the well. From these, POWeR‐FADS nonintrusively postprocesses time series of matrix and fracture water heads at the well, as simulated by any planar, bidimensional dual‐continuum hydrogeological model, to calculate water exchanges involving the observation well and thus the evolution of water level in the well. Synthetic test cases show that POWeR‐FADS makes it possible to simulate peculiar behaviors that are similar to patterns actually observed by the authors in on‐site observation wells of a fractured porous aquifer, like “floors” in observed water levels, delayed but sharp rises at the beginning of recharge events, or inflexion points accelerating the drawdown velocity during the recession phase.