You can use the double replacement as already suggested in other responses, but I would tend to prefer regex replacement, for concision of code:
yourString.replaceAll("\r?\n", "<br/>");
Or, of course Pattern equivalent, if you need to do the operation multiple times:
Pattern endOfLine = Pattern.compile("\r?\n");
endOfLine.matcher(yourString).replaceAll("<br/>");
Also, be careful with using System's line separator if user's input has been acquired from a web interface, or a remote system (depending on your use case, of course). User may use a different OS...
However, in all cases, make sure you do any EOL -> <br/> replacement, AFTER you have HTML-encoded any special characters in the user's input. Otherwise, the <br> tag will get encoded...