Very complex question and whilst everything that people have said so far is generally true there are many other things that have to thought through first.
To name a few:
1) What sort of process is being installed: The term water treatment plant is very generic but could range anywhere between a pump with a chlorinator to some sort of super advanced process with every bell and whistle possible that removes nuclear waste out of process water.
2) Who owns it: A municipal customer will have different requirements to say a mine , a power station or an industrial process. Some may want high reliability, some may want low price , some may want total unattended operation, some wont know what they want or need.
3) Size of the plant: You might be able to justify somethings from a cost perspective on a large plant that you might not on a small plant. However a small plant may have to operate with much less supervision than a large one.
4) Where is it: All the recommended things above are great for continental USA and probably most advanced countries. But the requirements in a less developed country will be totally different.For example there may be no requirements for SCADA , online monitoring and PLCs. Even if these are installed then there simply may be no back up or support for these systems. Water plants are still built in flood prone areas by necessity so that needs to be considered.
5) Energy efficiency: At a water treatment process level a lot can be done around energy efficiency but once it comes down to component selection some good choices have to be made as well. Often a lot of good work is wasted selecting a good pump with high efficeincy but then a cheap motor is fitted. Most of the energy usage in a water plant will be for pumping and in a wastewater plant for pumping and aeration. Therefore very high efficiency motors should be selected for any process that has more than occassional use within the plant. Cost impacts are relatively minor and easily recovered.
6) Maintainability: Think about the type/brand of equipment that is being installed. How easy is it to source. Will local labour be able to repair /maintain/program etc.
A couple of common issues that would seem obvious but often overlooked.
Segregate power from chemicals and water. Put power and instruments into a seperate room with climate control if possible.
Common equipment brand, sizes , models etc wherever possible throughout the plant: This will give a degree of redundancy when things go wrong, and will help if an item can be easily relocated to a more critical application. For example dont put multiple brands of instruments or VFDs or whatever simply because you can, or to get the best price.
Think about this. The plant will have to be maintained and operated long after you the designer are out of the picture. Dont just do something because its easy for you, but think about the person operating or maintaining the plant in 5, 10 ,20,50 years on.
Regards
Ashtree
"Any water can be made potable if you filter it through enough money"