Any PIMS software should suffice and the under listed analyzer should give you some decent analysis

 BR_nov AA Series from Analytik Jena 

Sanexen developed a software, TerraSysTM, for the ecotoxicological risk assessment on land and aquatic environments. Any substance, including metals, can be assessed using TerraSysTM . It is now marketed internationally and licenses have been sold in various countries in Asia, Europe and America.

http://sanexen.com/en/terrasys/terrasys-in-brief/what-is-terrasys/

software for heavy metal pollution study in water, kindly go through 

Evaluation of water quality pollution indices for heavy metals contamination monitoring in the water of Harike wetland, India. By  O.S  Brraich, S.Jangu- international journal of scientific research ...2015.

You may want to look at Query Manager. It;s a free application available at :

http://response.restoration.noaa.gov/querymanager

Query Manager is a database standard and query tool that can be used to access your sediment, tissue, water, and oil chemistry results, as well as standard sediment and water toxicity data. Query Manager can organize data sets from multiple studies into a consistent and standardized structure..

Users can sort and examine data in a variety of ways by selecting from a menu of pre-programmed queries. These queries allow you to evaluate individual contaminants and contaminant groups, plus make comparisons to common toxicological benchmarks, calculate totals, and apply toxicity models.

Mike, I have downloaded the software, but then how do I perform the heavy metal pollution indices with the data that I have?

Thanks. i am enjoying the contributions. Kudos to all.

Query Manager is both a data depository, and, has the analytical capability built in to query the data against benchmarks. Yes, the trick (or first step) is you must put your data into the format of database portion of the QueryManager application.

The database portion is essentially a collection of hierarchical  .dbf files:

study > site > station > sample > etc.

At the level of the analytical chemistry (chemsb.dbf for sediment), it can be a bit tiresome since each analyte is a separate record in the database structure.

QueryManager's real benefit is compositing different studies into one consistent structure, from which queries can be more easily made.

If you download one of the past projects (I recommend Vieques) you can see the database structure. Don't hesitate to contact the QuesryManager folks either.

Cheers,

Mike