I'd use a quite classical method: measure the time used by each query and write in a debug file the timings, followed by the query. Then, run the application a few times, in normal usage conditions, and see the queries that take more time.
About timing in Java:
How do I time a method's execution in Java?
Also notice that some SQL queries do take more time than others because of the quantity of data: for example, "SELECT" statements are common bottlenecks. A SELECT * FROM userdata
statement takes much more time than a SELECT name, surname FROM userdata
one, especially when you have lots of stored data.