The objective of the present paper is to develop a methodology that could allow the representation of the analytical hyporheic flux equation model (AHF) in a numerical model done in MODFLOW. Therefore, the scope of the research is to show the viability of the methodology suggested in a real case (Biebrza river, Poland, Europe). Considering that the model requires extensive manipulation in the creation of the packages, a test phase through the seepage package of MODFLOW is carried out with the aim of representing the river package of MODFLOW. FloPy is the tool chosen to develop this implementation due to the versatility of manipulating the packages available in MODFLOW through coding. The obtained results showed a correct implementation of the AHF model using the example of the Biebrza River. The results obtained will enable a better understanding regarding the modelling of the interaction between the river and the aquifer, considering streams with specific geometries where the depth is dimensionally higher than the width.