The "Prison Break: The Classified FBI Files - Official Companion Book" reports that recovery of the data on the disk was actually highly problematical, but ultimately succeeded due to the cleverness of law enforcement.
Since spending millions of dollars dredging the river is massive investigative overkill, even for the crime committed. I think we can reasonably assume that Michael simply felt that throwing the hard drive into the river would be sufficient to dispose of it forever. He obviously didn't bank on the involvement of the FBI or the resources they were willing to bring to bear:
A search of Scofield's home revealed no additional clues to the
fugitive's plans. However, one wall was filled with holes that seemed
to have been made by dozens of push pins. Mahone concluded that
Scofield had made extensive plans for the escape prior to his
incarceration and then designed them into the tattoo. Since Scofield's
home was close to the Chicago River, Mahone ordered that the river be
dredged, suspecting that it was a prime location for Scofield to have
dumped the evidence. A hard drive was recovered from the river, and
the serial numbers matched an order that Scofield had placed with Dell
a few months before he was incarcerated. Files found on the hard drive
revealed additional information important to the investigation, as
detailed elsewhere. It took some time to recover all the data.
Note also that the serial numbers (and the make of the drive) would probably have been sufficient to provide a circumstantial conviction even had he drilled or microwaved the HDD to remove the data.
It's also worth pointing out that (in the real world), unless one is willing to invest a very considerable amount of resources, a hard disk that is submerged for even a few minutes is largely unreadable and one that is submerged for 6 or more months is generally (but not always) considered to be beyond any sort of repair.
