During the Renaissance, there were six bridges built over the Tiber which allowed civilians to cross the river from various points within the city. Among these bridges were the Ponte Sant'Angelo and the Ponte Sisto.
However, only two of these bridges crossed the river to Tiber Island; both of which were marked with the Templar cross. No other bridge in Rome had these symbols, despite Tiber Island housing an Assassin headquarters.
Ezio Auditore da Firenze considered dropping the Apple of Eden into the Tiber after a confrontation in the Vatican in 1499. The following year, he re-established the Assassins' headquarters in a store room on Tiber Island, which had several tunnel entrances underneath the city of Rome. It was also possible for Ezio to enter the headquarters by diving into sewage tunnels that fed from the island into the river. 
It was the habit of Cesare Borgia to have the bodies of his enemies discarded into the Tiber, including that of his brother Juan Borgia the Younger and Francesco Troche. In 2012, the Templars continued this practice by dumping Clay Kaczmarek's body in the Tiber after his death.