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The full transit goes all the way from Atlantic to Pacific (or vice versa) and they usually are longer cruises, involving repositioning (although not always). Partial transits are typically from the Atlantic side, and involve going up the set of Gatun locks, into Gatun Lake, and then returning through those locks again to the Atlantic side. You get to experience the going up and down the locks, but you miss out on the sailing through the narrow waterways to the other side.
It gets quite hot down there, and we went in January. That's probably when I would go again if doing a partial. If doing a full, I would likely do a spring repositioning from the east coast to the west coast if only because the fall is still hurricane season.
"I'd Rather Be On A Ship With A Drink On The Rocks, Than In The Drink With A Ship On The
Fond Memories Of
Carnival Dream - Western Caribbean - Jan 2013
Navigator Of The Seas - Western Caribbean - Jan 2011
Carnival Pride - Grand Turk and Bahamas - Twins First Cruise - Aug 2009
Caribbean Princess - Eastern Caribbean - Jan 2008
Sapphire Princess - Mexican Riviera - Jan 2006
Carnival Victory - Canada/New England - Sept 2001
Carnival Tropicale - Panama Canal - Jan 2001
Grand Princess - Eastern Caribbean - Nov 1999
Westerdam - Honeymoon -Eastern Caribbean - Nov 1995
Panama has two seasons:
The rainy season in Panama is from May through November and the dry season is December through April. During the rainy season it typically rains every day. During the dry season it is unusual to have any rain.
If your focus is to see the Canal, I would recommend a full transit, now let me insert a "but" here! There are some great advantages in taking the a partial transit cruise. Nomally, once your ship reaches Gatun Lake after passing through Gatun Locks, a tour is offered that takes you on a partial transit of the Pacific Locks and Gaillard Cut. By taking this tour you will have been through a large portion of the Canal, plus you will have the benefit of seeing the operation from the vantage point of your Panamax ship and then from a smaller vessel as well. A great comparison and I believe that the Pacific Locks and Gaillard Cut have more of a visual impact.
Using weather as your only factor, probably the best time is January through mid February. This is when the temps and humidity are at their best... a word of caution, anyone coming from a temperate climate is going to think the humidity is high! This would be particularly true coming from where it is cold and jumping right into the tropics. Use this as only a tie-breaker since the differences will only be slight
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S.S. Badger R/T from Manitowoc June 02
Wife and I cruised the canal in October of 2008. We prefer the full transit. As for the weather, we got a bit of everything. It was very humid, close to 100 degrees, sun was shinning, then thunderstorms rolled in. What ever way you choose to go you are going to see a wonder of the world, its amazing.