What you need to look for is all the Water Quality data that you need to represent using GIS. After data collection, the required GIS analysis processes should be undertaken. The outcomes are represented by geographical maps shows quality parameters distributed in zones throughout the processed maps.
As said by Noor M. Al-Kharabsheh you first need to perform the data collections (and then think about analysis to undertake....). for this purpose, for Sea Water parameters there is a remote sensing data available directly from Quantum GIS.
GIS is an important technique to determine spatial and temporal variation of ground and surface water quality. When you studying river basin management studies, You can overlay aquifer maps, contours maps, land use maps, population, agriculture or any other related parameters with each of the water quality parameters and interpret your results and predictions.
For surface water quality, you can use interpolation techniques for only the part of river you studied or use symbology technique for sampling locations.
Hope following paper will help you for getting information,
Article Mapping Spatial Distribution Of Water Quality Parameters Usi...
GIS is a mapping software. Basically you need the water quality data to start with. Using the GIS soft ware and making use of the water quality data, spatial and temporal variation of water quality parameters, through interpolation technique, can be prepared. Thereafter using other spatial maps such as geology, aquifer parameters, land-use, point and non-point pollution sources, etc., one can interpret the source and reasons for water quality.
it is clear that you can use remote sensing data, but an useful method for estimating water quality value can be exergy analysis. as last researches, you can calculate the quality of water by considering two options: 1- the BOD,COD and .. analysis by using remote sensing data.
2- using exergy analysis for analyzing these data.
I think you need to identify water quality parameters, prepare thematic maps for each parameters, and finally use spatial analyst tools to get final map for the most/least vulnerable sites.
Water samples have to be analysing then the values enter in to excel file GPS location then open arcgis and import this file then do georeference. Then u can generate water quality analysis using inerpolaton tool(this tool used to find out the unknown sample site water quality parameters value from known samples