Crystal Springs glitch
On Crystal Springs, normally you would need to find a song to break the rocks to complete the level. However, the entire task can be skipped, just swim inbetween the bottom two rocks and keep tapping B and C, and wobbling the directional pad and you will pass straight through.
Dark Sea glitch
To skip a large portion of Dark Sea, when you have opened the first spiked gate below the save point, enter the ship and head left then down. In this room should be an invincibility crystal. Go to the very the top right corner of this room, then quickly swim left using B and C, and you should pass straight through the wall. Once you pass through, quickly swim to the upper left of the screen to avoid being crushed.
Hard Mode
In the starting area break the two shells above you, and then swim through the tunnel to start the game in hard mode.
Level select
At the beginning of the level there should be 2 rocks. Face up toward them and press B (they will break). Swim through and you will be in the first level.
Turn so that ecco is looking at you. While he is looking, press start and quickly press A, B, C, B, C, A, C, A, C, A, B.
Secret Hungarian Language
On the language select screen press the following buttons: - While hold down A button: left, right, up - While hold down C button: down, right - While hold down B button: down, up If you entered correctly, the hidden language option hungarian (magyar) is pop up. Works only with the PAL version of the game.