I need to construct my 3D conceptual model considering the geometry (boundary conditions), topography, fluxes (precipitation, evapotranspiration, runoff, etc.), flow directions and so on...
I highly recommend you try ModelMuse which is a completely free software that was developed by the USGS and comes with a free GUI making it easier to build your conceptual model.
All of these answers are pertaining to numerical modeling not conceptual modeling. Typically you "construct" your conceptual model based on site and literature data (e.g., climate, topography, surficial geology, geological structure, boreholes, wells, surface water, groundwater water levels, recharge areas, discharge areas, aquifer testing, etc.). The conceptual model is typically composed of text and figures in ArcGIS or equivalent. Then, you can develop a 3-D numerical model based on your conceptualization of the groundwater system using the programs listed above.
Walter Antolinez that helps. We typically use Adobe Illustrator, Leapfrog, or MVS, which are not freeware, to put together graphics like this. I suggest looking at this researchgate thread that covers this topic: