I wonder if you're considering just general groundwater or tile drainage system is also in part of your work? If so, maybe you can try SWAT (can be initialized by ArcSWAT). In addition, it has been linked with other groundwater model such as MODFLOW. I wouldn't say it is the best choice but not a bad one to start with. 

 Dear Haw,

Thank you for your kindness.

I am going to model groundwater potential in ArcGIS. In General we consider some factors which are effective on the groundwater quantity such as altitude, slope angle, lithology, land use, etc. 

I want to add some quality factors' map to my work and make it more comprehensive. I'll appreciate you if you introduce me some water quality factors which are more important...

Best

Water quality is a broad area, and you might narrow or specify your focus.

If the type of water quality you are interested in is inorganic, you might start with total dissolved solids (TDS). Then you might see if you can evaluate the major cations and anions. You can classify water types by the major cation ( calcium, magnesium, sodium, and potassium) and anion (sulfate, chloride and carbonate species). A piper diagram is a graphical method https://en.wikipedia.org/wiki/Piper_diagram and there are free programs listed in the wiki page by USGS that can assist.

If you are concerned about water quality impacted by organics from waste water releases, you might evaluate " fecal coliform"  https://en.wikipedia.org/wiki/Fecal_coliform which is a common indicator for water quality impacts. Nitrogen is another that may indicate waste water or agricultural water quality impacts.

I suggest you review a book or review paper on water quality, and find out what data are available to use and potential water quality problems are important to your area of study.

Seyed,

Your question is 'modeling groundwater potential' for which GIS model is possibly the best technique. MODFLOW and similar s/w are basically predictive models that would give you futuristic ground water scenarios. These models would help you essentally to know what would happen to the ground water table with certain stage of ground water development. They may not present well the quality aspects of ground water potential in various scenarios. But, you could very well make the trend analyses of both ground water levels and quality parameters to get some futuristic scenarios from quality prespective. The trends of the quality parameters could be drawn independently too. But, it would be good to use both these trends together simultaneously to examine the hypothesis that decline in ground water level leads to quality deterioration. The fact is, rise in ground water table too leads to quality deterioration.

You could possibly make sevaral GIS layers of the water quality parameters individually, as suggested above, and superimpose them with other different kinds of layers that you would construct to assess the ground water potential, such as soil types, depth to water levels, rock types, aquifer parametrs, crop types, etc. and make the final analysis of the ground water potential.  ArcGIS is the best technique that way. You could possibly use ROCKWORKS too to get some 3D picture of your aquifers if you have assess to litholog data of some drilled wells in your area. Some kinds of 3D aquifer vulnerability maps could also be prepared of you have depth wise quality parameter data (such as EC/salinity) available.  

Water quality parameters to watch for generally are EC and Na from irrigation water quality perspective. Ca, Mg could possibly give you information about the hardness of the water. Other paramers such as Fe, F, NO3 would be important from drinking water perspective. From heavy metals, please look especially for As, U, Se etc. Please superimpose layers of these parameters with the other types of maps that you would generate through GIS or otherwise to examine the quantitative aspects. I am sure you would get a better picture of the ground water potential of your area if you would combine both types of maps (quatitative and qualitative) however generated they are. 

I wish you lots of Luck..

Dear Kenneth and Pradeep.

Thank you so much for your useful comments and suggestions. I received very useful information for my project.

Yes of course you can model groundwater. But perhaps you should consider these:

If you have complete geochemical analyses from boreholes (physical parameters such as pH, conductivity, Oxygen etc, and chemical loads such as NO3, NO2, PO4, SO4, alkalinity, hardness, major elements such as Ca, Mg, K, Na and perhaps Cl, basic metals, trace elements, radioactive elements etc etc, you can have a direct and perfect comparison with the quality of your groundwater with Water standards applied in your country (e.g. Europe, a nation, USA etc). Regarding quantity this is more tricky because you have to combine annual precipitation data, infiltration data, runoff data and evaporation data (all annual), in order to estimate the water balance in your area.

After you got these you can model considering Climatic scenarios, CO2 scenarios etc. The more annual data you have you can calibrate well your model.

But when you want to predict what will happen if a pollutant enters groundwater (by industrial, domestic or other facilities), and you want to model it you need a pollution modeling software such as FeFlow . If you manage to control FeFlow you got an opportunity to either estimate with much confident or get a good job around the globe. Take care and best luck with your research.  

Dear Seyed,

This is a broad question and a complex problem. Good for you for going after it! I suspect you'll need to piece various works together to make decisions how to proceed. We've had good luck with Modflow (and a few other models) recently, but I also found that given the complexity of the question we needed a rich observed dataset to work from. The data (as you know) are often very difficult to find, so we designed our own study and have published a number of papers recently that I hope might be useful:

Kellner, E., J.A. Hubbart, A. Ikem. 2015. A Comparison of Forest and Agricultural Shallow Groundwater Chemical Status a Century after Land Use Change. Science of the Total Environment. 529:82-90. DOI: 10.1016/j.scitotenv.2015.05.052. 

Zell, C., E. Kellner, and J.A. Hubbart. 2015. Land Use Impacts on Subsurface Floodplain Storage Capacity: A Midwest Case Study of Agricultural and Remnant Hardwood Forest Land Use Types. Environmental Earth Sciences. DOI: 10.1007/s12665-015-4700-4

Kellner, E., and J.A. Hubbart. 2015. Agricultural and Forested Land Use Impacts on Floodplain Shallow Groundwater Temperature Regime. Hydrological Processes. DOI: 10.1002/hyp.10645

Kellner, E., and J.A. Hubbart. 2016. A Comparison of the Spatial Distribution of Vadose Zone Water in Forested and Agricultural Floodplains a Century after Harvest. Science of the Total Environment. DOI: 10.1016/j.scitotenv.2015.10.080

Hope that helps. Have fun and best of luck!

Jason Hubbart