No, you do not need to create multiple projects to use waterfall method. Simply create a project and design a waterfall workflow. Then you can create your issues and change the status depends on the phase.
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In JIRA there are feature called Linking Issues..
http://confluence.atlassian.com/display/JIRA/Linking+Issues
..but the structure is flat and there is no option to indicate that issue cannot start till previous is completed. This is only an information for you (like "blocks by") that the dependency exist.
Of course you can use some third party plugins (addons) that support structuring and dependency relations. OOTB this it not available.
There is an issue that cover that feature..
https://jira.atlassian.com/browse/JRASERVER-1383
It is currently "Gathering Interest" so there is a chance that it might be implemented soon. I suggest you to vote and watch i if this is an important for you and your process.
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