A complete methodology for groundwater flow and solute transport modeling is described step-by-step. Definitions, terminology, and a general methodology are proposed. Emphasis is given to the conceptual model choices involving processes to be simulated, parsimony versus complexity, dimensionality, and specific choices linked to fractured and karst media and for modeling interactions with surface waters. Initial and boundary conditions for groundwater flow and solute transport simulations are described and discussed. Model design and data input are addressed with a description of the different input data. Calibration, validation, sensitivity analysis, and inverse modeling are summarized in both deterministic and probabilistic frameworks. Geostatistical aspects and stochastic/probabilistic techniques together with uncertainty analysis are summarized for practitioners.