Yes - the water table does replenish

The water table in SimCity is replenished from the following sources;

• Rain
• Water from shorelines
• Sewage treatment plants
• Other cities
• Outflow pipes from industrial buildings

Rain is not a reliable source of replenishment but does contribute. Due to its random nature (it never rains when you want it to) you should never rely on your water table being replenished by rain. Water from the shorelines however does replenish the water table a lot faster than water from rain, but seemingly not fast enough to cater for a sudden explosion in population.

The outflow pipes from industrial buildings will put polluted water back into the ground. This doesn't show up as blue but even so, it is still water. It will need treating before it gets to your Sims but it is still present on the water table.

Sewage Treatment facilities will replenish the water table during their normal operation. Sure they're pretty expensive to place but if you're heading towards a high population city you will need to cater for replenishing the water table just as much as getting garbage off your streets or keeping everything powered.

Some tips for managing your water

• SimCity is not SimCity 4 - large cities are not supposed to be self sufficient. This is managed by the 'multi-city' game mechanic and if you want clean and efficient cities with large populations you are going to have to import some of your water
• See water management as a challenge you're going to have to overcome along the way through proper planning and preparation
• Slow down! The purpose of the game isn't to get a massive population in as little time as possible, the goal is to create a stable region consisting of multiple cities that compliment each other
• Some cities may be your population centers and some cities may be mining hubs, and these cities are going to be thirsty, but other cities in the region may have an abundance of coal or oil, and these smaller cities can provide the water to your population centers

The best advice for a perpetual water supply

Build a water pump next to a sewage treatment plant. The sewage treatment plant will replenish the water table as fast as the water pump is depleting it, thus providing the effect of infinite water. It's also a good way to pick up germs and make your population sick in the instance of a sewage overflow, so filtration pumps at your water pump may be the way to go with this.

From the EA store page:

More Transportation

Transport your Sims more efficiently with an exclusive Double Decker Bus station in Britain and high-speed rail in Germany!

It seems like the German vs regular train-station for the same cost (upfront & maintenance) for better performance.