Bottled water does not have to be transparent. There are some companies that do not use transparent plastic bottles. Not all companies use plastic either but environmentally sustainable polyethylene terephtalate or rPET and polyethylene terephtalate or PET bottles that are BPA free and can be recycled and are a more pragmatic choice. Glass is an expensive option given the nature of the business.
Very few companies opt for translucent or opaque bottles. It is not deemed viable since people prefer the lucid appearance of bottled water. It is hence almost imperative for you to go for a standard transparent bottle for your product. Of course you can experiment if you wish. The custom label is a different matter though.
While there is no reason for any company to adhere to a norm of choosing a particular color for bottled water with custom label, you would notice that blue has been the most widely associated hue. Most labels of bottled water use some shade of blue. There are some companies using green or blend it with tinges of blue.
A few companies have gone for shades of pink. Black and red are found but are relatively rare. You will indeed find a wider spectrum of colors or shades of popular hues but the most common ones are confined to two or three. You can go along with the trend or buck it and come up with something entirely different.
You may or may not succeed with your experimentation of bottled water with custom label as far as changing the color of the container is concerned. It is safer to go with the standardized transparent look. However, you can always experiment with your choices regarding the color of the custom label.
This has nearly no bearing on the actual appearance of the water in the bottle, since people can see through the plastic anyway and get that lucid view of the water inside. Choosing an interesting color to go along with the information on the bottled water with custom label can be an effective way to stand out in the crowd.
There is only one limitation, rather a prerequisite and that is visibility of information. You cannot choose a color that would make the information on the bottled water with custom label difficult to comprehend or nearly ineligible from a fair distance. This is one reason why many companies play it safe with the tried and tested colors but you can always explore more hues for the printed information so they complement the shades of the label.
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