You can leave your friends a message or respond to a message left by a friend by using Fish Mail. Fish Mail is located in the fly out menu that opens when you click the orange gear on the toolbar below your tanks.
Fish Mail works like a message board. You can post messages in your own Fish Mail, or visit a friend and leave a message for them in their Fish Mail. Messages posted can only be viewed in the tanks of the person where the Fish Mail was posted. Thus, if you leave a message for your friend and they respond to that message in their own Fish Mail, you could only read their response to you by going back to their tanks and re-opening their Fish Mail.
If you receive a Fish Mail from a friend in your game and you wish to reply to it, click the name of the friend who left the Fish Mail to load their game. Then open their Fish Mail by clicking the orange gear on the toolbar and then clicking the blue Fish Mail envelope. Now you can leave your friend a reply that they will see when they open their game.
You can also click on the envelope, write a message, click X instead of post, move to the next tank, click on the envelope again and your message is still there. I find this helpful in making it easier to comment on seperate tanks. Then hit post when you are done.
Fish mail is basically a message board for your tanks. When you visit your neighbor, you can leave a message for them. Likewise, they can leave a message for you and you can respond to their messages. Your fish mail appears the same no matter what tank you happen to be in. Newer posts are listed first with older posts listed beneath them. You can delete posts on your own Fish Mail and you can delete your own posts from others fish mail. Fish Mail is not an instant messenger.