I hope this will be helpful to you.
Engr. Mansoor Ahmed - PhD. Scholar Environmental Engineering
Master of Engineering Environmental Engineering
Chief Executive - Post Graduate Certified PMP, Advanced PM email@example.com
Hi, there was a discussion on this top in the Linkedin Hydrogeology Forum, I have included a few of the comments given that are relevant to aquifer modeling and GIS. Modflow is the popular and best documented. GRASS would be my second port of call.
I got message from Vishkha Rajput about your question. There are many freeware and opensource software are available on Internet. Like MODFLOW, ModelMuse, PMWIN, Hydrus etc. These are freely available and you can use for it aquifer modeling.