That even seems within the range of variation of the water level. Google suggests [0] the water level rose 6m between 1943 and 1986 and generally fluctuates 1m or so each year. If that's typical, the box could have been at shore level, or well above, or 20m below in Inca times.
[0] https://link.springer.com/referenceworkentry/10.1007%2F978-1... (source is paywalled for me)