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This map will show you the nearest large lake to Engelberg that has lake boat rides is Lake Lucerne.
You will pass through Luzern ( local German spelling) on your way from Venice to Engelberg. The direct trains from Luzern main station to Engelberg run at xx10 and take 43 minutes; last one at 2110.
Later trains run at 2127, 2227, 2327, take 49 minutes, and require a change to a bus at Dallenwil.
Trains from Engelberg to Luzern main station ( where you would catch boat unless there is some clever way to pick one up at an intermediate stop, which would require careful study of maps, schedules and stations to determine. Not recommended if you are tired.) run once per hour at xx01.
Assume you arrive at Engelberg at 1553, get to your hotel, eat something, and manage to get on the 1801 back to Luzern. You will arrive at 1849.
Here is the lake boat schedule. Make sure you select the correct seasonal timetable -
Find a boat ride. There is very limited service a that time and afterwards. I am not sure what boat you would take. An obvious one to go to Alpnachstad, where you could pick up a train that would get you on your way back to Engelberg has it last run at 1812.
However, lets assume that somehow you found a boat ride that would get you back to Luzern main station at 2049. ( two hours for the ride) . You could catch the 2110 back to Engelberg and be there at 2153.
I don't know what boat ride you would find, but it is technically feasible to do something like your suggestion, since you could even take more time at Luzern and still catch a train back to Engelberg as late as 2327.
Would you really want to do that? I'd guess it would be tiring after a long day, but,that is up to you.
By the way, I got all the train timings from the timetable:
An option would be to pause on your trip through Luzern and take a break on a boat ride. Presumably, you would be at Luzern at approximately 1500 on your journey from Venice. You could leave your luggage in lockers, or, possibly at the left luggage office ( check hours of operation....close at 1900 I think). There is a good choice of boat options, depending on how long you wish to make your break.
Hope that helps.