Can you please suggest me the name of software which is generally used to analyze water quality. It should be free of cost to use it. if you know such type of software please informed me in below comments.
Water Quality Analysis Simulation Program ( WASP) is most common software and it is simple to use for water quality study. Detailed study well published and also available on line.
It depends up the type of data, what you want to do with it, and the sophistication of analysis required.
I do my work in R. It will handle all kinds of basic analyses. But it is difficult for a beginner to learn without good examples. You might start with http://www.biostathandbook.com/ or http://rcompanion.org/handbook/ for examples of common simple analyses.
You might also look at the USGS EGRET software. I haven't used it, but it looks promising for some kinds of data.
I also agree WASP seems very cool. But just to give you other options if you'd be working with metal, good simple models for chemical speciation are well described in the current version of VisualMINTEQ. If you work with a river and need to deal with the transport of contaminants there is also the PHREEQC. Finally, I have also used for more complex systems (i.e. watersheds, rivers entering lakes or estuaries) the water quality mode in the software suite of Delft3D. Links to documentation and download of these programs follow below.