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Coupled flow and heat transport models are essential for understanding subsurface processes and for assessing the long-term sustainability of deep geothermal systems. Due to its favourable geothermal conditions, the South German Molasse Basin, characterised by the fractured and karstic carbonate Upper Jurassic Malm aquifer, is Germany’s most productive geothermal region. Extensive development has made numerical reservoir modelling mandatory for permits and critical for assessing project viability and impacts on nearby plants, supporting informed decisions by both operators and authorities. This study presents an analytical review of geothermal reservoir modelling methodologies applied at 22 existing geothermal plants in the South German Molasse Basin. We examine how key geological features, including stratigraphy, faults, karst horizons, and lateral facies variations, are represented with different conceptual and numerical approaches, from explicit structural integration to effective or homogeneous parametrisation. We systematically evaluate the strengths and limitations of prevailing modelling approaches, benchmark them against state-of-the-art methods, and identify key methodological gaps. We further analyse how subsurface data (e.g., pressure, temperature, porosity, permeability, and inflow zones) are incorporated into models and classify parameters by their level of constraint (measured, derived, calibrated, or assumed), enabling consistent cross-comparison. We identify a wide range of modelling approaches, largely due to geological heterogeneity within the reservoir. Calibration practices also vary significantly, with most studies focused on hydraulic calibration with pressure data, while thermal calibration based on temperature measurements remains rare. We also discuss methodological limitations, including the absence of uncertainty analysis of model outcomes and the limited use of operational data for model validation. These factors influence model predictions and have implications for the long-term sustainable management of geothermal resources. By synthesising reservoir modelling practices and contextualising them within state-of-the-art approaches from other sedimentary reservoirs, this review provides a reference framework to support more consistent, transparent, and robust geothermal reservoir modelling and to facilitate knowledge transfer across sedimentary systems.