I am looking for a free and open source software (such as GCDkit) that I can use to normalize my groundwater data. As of right now, I only know of GCDkit and IgPet which both only normalize rock data (ppm), not water (ppt - ppb).
I am not specifically aware of any programs or software to automate, but some basic work data transformation and analysis work can be done in Excel. There could be several ways to normalize or transform data, and it is probably best to know more about the specific data and intention. If you have water table data, you could normalized the water table elevation data in comparison to the mean water table elevation. So water table elevations above the mean would be above 1.0, and water tables below the mean would be less than 1.0. If you have data that extends over several orders of magnitude, transforming using logs is often suitable. Exponential curves help handle data that levels off. Statistical packages may have some tools that can help design, and address factors in multivariate analysis. There may be reasons to stratify data, and certainly becoming aware of any groundwater literature that applies to your area of interest may give you other ideas or examples.