There are a variety of products that can be used.
EZ-Water and it's brethren ilk need to be heated and thus care needs to be taken when pouring it as it can warp bases, destroy detail, etc(talking form experience).
Other like acyrlic gel and similar, don't generate heat but need to be poured in thin layers and each layer needs to dry.
Your local arts-supply and and Model Rail Road store should have plenty of goodies to work with.
Two more thoughts:
Depending on how clear/muddy you want the water it might be better to work with putty, texturing gels or similar. No using buying stuff for clear water and than painting it so that the translucency is lost.
Rather than tinting the medium or painting the medium in the water colour, I have found that I get better results painting the base prior to adding the water(muddy water works differently though).
The clear medium will still show the colour and at the same time you will get a better feel for depth, plus you can add items into it like fishes, etc.
In the end what medium you use will also depend on the amount of water you want to create/simulate.
HTH.