Identify the query or queries that are taking a long time.
Observe their locking, blocking and wait statistics behaviors. That might tell you what's wrong.
Look at their execution plans. That might tell you what's wrong.
Fix what you need to fix.
Other than that, this is a very involved topic. For lots of detail on how to get this done, get a copy of my book on query tuning, linked below.
"The credit belongs to the man who is actually in the arena, whose face is marred by dust and sweat and blood"
- Theodore Roosevelt
Author of:
SQL Server Execution Plans
SQL Server Query Performance Tuning