I replaced my roof marker lights and sealed the new ones, Still there, Windshield leak?

I have a 2003 dodge ram 3500 quad cab (4 doors) I have developed a leak in the cab and there is water pooling up in the small storage space under the rear , drivers side seat. The water is pooling up and i have no idea where it is coming in from. It is making my cab stink, which is causing my wife to complain and is leaving mold in the carpet, which is not good for me the wife or my kids. If anyone has any solutions to this problem, please, let me know.