There are three things to consider - the ISession object, the SQL queries that are generated and your plain-old-clr-objects that are mapped to tables.
NHiberante will generate the required SQL queries based upon the chosen database dialect. If you configure NHibernate to use the SQL Server dialect it will generate SQL server correct SQL statements. This can easily be configured dynamically at runtime based on configuration.
You also need to configure your session to connect to the right type of database. Again, various configuration methods can support dynamic ISession creation at runtime.
Your actual data objects which are mapped to tables should not need to change based on database choice. One of NHibernates strengths is flexibility it provides in supporting multiple databases via a (fairly) simply configuration change and some up-front architectural thought.
See http://codebetter.com/blogs/karlseguin/archive/2009/03/30/using-nhibernate-with-multiple-databases.aspx for some examples of how you might abstract the underlying database away from the creation and usage of NHibernate.