I am leaving in July for the Inner Passage on a small boat cruise with National Geographic/Linblad Expeditions. In our packing list, we were advised to bring knee high rubber boots. I am hopeful that someone that has been on this trip or on a similar one can provide some advice-- are the boots just for getting on and off the zodiac or are you expected to wear the rubber boots all day? We are hoping to participate in the hikes but wouldn't be comfortable doing this in the rubber boots. Is it possible to wear the boots to shore and then change shoes? Would you then have to carry the rubber boots all day? Any advice you can provide would be greatly appreciated!!
Also happy to hear any other advice you can provide on packing. We know there is no need for formal dress but are also trying to be very compact in our packing. We are avid travelers but have never been on a cruise before.

Since trails can be pretty muddy when you're somewhere that rains a lot, and along the edge of the water... I'd guess it's for walking.. Sometimes you need a boot that protects you from sinking in below your ankle. Note this isn't for your particular tour.. so you may want to ask them.

If you have properly sized boots and thick socks you should be able to walk in them fine, sometimes I'll get the next size up and put an orthotic insole inside.

You may also have some walks where you can get away with regular hiking shoes (hopefully waterproof).

you might try looking for rubber boots at a farm and feed store where they carry brands for people who need to wear them all day. Or, you might check with the cruise company to see if waterproof hiking boots with gaiters would be sufficient.

First, it's the InSIDE Passage.

I looked on Cruise Critic's Lindblad board - https://boards.cruisecritic.com/forumdisplay.php?f=23 - for any trip reports that covered the question, but couldn't find any. (I didn't look all that hard.) Looking at Lindblad's day-by-day schedules (don't know which applies to you) it looks like most of the days you'd need boots ("Wellies" in BritSpeak) are those where you're kayaking or using Zodiacs to go ashore outside of the towns. In those cases it sounds - could be wrong - like any hiking would be fairly short; presumably the guides know that rubber boots are not so hot for long walks.

Where are you joining the cruise? You might be able to get away with buying some boots before you sail, thereby simplifying the packing list.

"You may also have some walks where you can get away with regular hiking shoes (hopefully waterproof)."

Not hopefully. You had better bring waterproof hikers if there are hiking days. And a waterproof jacket.

We have been on Lindblad expeditonary cruises in Alaska. You will need the boots on at times when transferring from zodiac boats to the shoreline for hikes in the rain forest. There is muck that you have to navigate. We didn’t wear them too often but they were needed. Still have them!
We sailed from Juneau to Sitka,a week long, and I can’t imagine sailing with any other company. Our ship held 70 passengers. We saw so many whales and the captain would change the itinerary to follow them. We used kayaks, hiked in rain forests and stopped at small villages. Only saw one large cruise ship while in Glacier Bay.

Thanks to everyone who responded- it was very helpful. I just wanted to make a note after our trip in case anyone else came upon this thread later. One day there was an option for a short hike- it was very muddy and tall boots were essential because there was a lot of sinking in the mud above the ankle. If you didn't have the boots, you could do another activity instead of the hike. Otherwise, you could manage the trip without the boots if you really didn't want to take them. There were a couple of times that you had to step out of the zodiak into the water before getting onto shore but waterproof boots weren't essential in that case-- you could wear a sport sandal or the like and then change when you got to shore into a hiking shoe or something else.