Travel route Gatwick to London to Windsor
 

I'm flying into Gatwick but would like to visit London before I arrive in Windsor. I'll only have one day to sightsee in London. I was thinking of taking the Gatwick Express into London. I believe it arrives at Victoria Station. Would I be able to check my bags in there and then how would I get to Windsor at the end of the day?

yes, you can check your bags at Victoria. But trains to Windsor leave from Waterloo or Paddington, so I'd instead take the train to Victoria and a cab from there to Waterloo. Leave your bags at Waterloo and then you just have to retrieve them before taking the train to Windsor.

The cab ride from Victoria to Waterloo is not very long and shouldn't break the bank.

Some will recommend taking a Thameslink train from LGW to London Bridge and the tube from there to Waterloo. That works too and would be a bit cheaper. It mainly depends on how much luggage you have and if you can manage it in the tube.

I personally would go to Victoria and then the cab.

Two other options almost touched on by Janis:

1. Take a Thameslink train to London Bridge and then take a taxi to Waterloo (not very far at all, no need for tube travel and through relatively quiet roads).

2. Take a Thameslink train to London Bridge, get off and wait on the same platform for one of the (very) regular trains one short stop to Waterloo East and then walk through the pedestrian tunnel to the main bit of Waterloo station.

I looked online and Saw National Rail trains that left from Victoria Station to Clapham Junction and then to Windsor. Is that a possibility?

You would have to change trains at Clapham Junction. That change will involve stairs. If that is not a problem, yes, it is a possibility.

Clapham Junction is the largest and busiest station in the UK. Yes, you can change there. I don't know which platforms the Victoria and Windsor trains use - but the two times I've changed trains at CJ it seemed I had to walk miles. It wasn't actually that far but was across several platforms and two flights of stairs..

Personally, I think the Gatwick-London Bridge-Waterloo option the easiest. At Waterloo East, you will have some steps to go up and then a longish elevated walkway to an escalator down to the main concourse. Left luggage is between platforms 11 and 12, within a few yards of the escalator. The signage for finding your train to Windsor at the end of your sightseeing is pretty clear.

Clapham Junction is a very busy interchange; though the walk between platforms is probably about the same length as at Waterloo, the signage is not so good, and you'd have to find your way up and down some very narrow staircases. Plus you'd be manhandling your luggage at the end of a long-ish day, whereas the first option gets the worst of that over at the beginning.