Slugs of free water in diesel fuel will kill an injector pump in a VE (rotary) pump TDI or a HPFP in a CR TDI in no time at all. In a worst case scenario the damage can be done in a matter of minutes.
From the OP's description of what happened, it sounds like the station where the car was fueled up at doesn't get much diesel business and the water accumulated from condensation. There might have been a problem somewhere and allowing rain water or melting snow to contaminate the tank. It's also a sign that the station doesn't regularly check for water in the tanks.
Hate to say it but I think the damage might already be done to the injector pump. Hopefully it's just a matter of getting the contaminated fuel outa there and refilling with fresh diesel fuel. Also suggest using an additive such as PowerService Diesel Fuel Supplement (white bottle) to help increase lubricity and to take care of any remaining water. If everything seems OK afterward it may be OK or the injector pump may fail after a while.
In general, water in diesel fuel = VERY BAD(!)
and is to be avoided at ALL costs. This is why I recommend fueling up only at busy high volume / high turnover stations that do a lot of diesel business. (Gasser business doesn't count.) Truck stops and busy gas stations along major routes are best. Go where the big rigs go. Basically get your fuel where everybody else does in your area. Fuel turnover is highest at these stations and is constantly being replaced, often daily. It is the freshest fuel you can get in the area. It is not uncommon for a busy truck stop along a major route to do more than $30k worth of diesel business in a single day. Whatever you do, avoid fueling up at stations out in the middle of nowhere that rarely get any diesel business, no matter how tempting the slightly lower price per gallon may be. A single tank of water contaminated fuel is all it takes to do a lot of damage. Not worth the risk IMHO.
Water in diesel fuel = VERY BAD!
AVOID it at ALL costs!
Good luck.