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How to resolve SQL timeout error in a window service application?

I have a web app which has been added as a reference to my window service app. The service will call a method in the web app which then will invoke the database to run a stored procedure.
I received an exception while calling one of my store proc. The stored procedure will approximately run for 45 seconds. Below is the error
System.Data.SqlClient.SqlException (0x80131904): Execution Timeout
Expired. The timeout period elapsed prior to completion of the
operation or the server is not responding. --->
System.ComponentModel.Win32Exception (0x80004005): The wait operation
timed out
I have tried to increase the service app timeout by appending ';Connection Timeout=3600' to the service app conn string in web.config but the exception still occurred after around 30 seconds of running.
Your help to resolve this issue will be greatly appreciated.

To elaborate on #Squirrel comment:
Your error message shows a System.Data.SqlClient.SqlException. So the timeout is on SQL Server side.
So if you want to increase the timeout, it must be done on the SQL Server side.
In the System.Data.SqlClient namespace you seem to use, the SqlCommand class that you probably use to call your stored procedure has a property CommandTimeout that let you set the timeout value.
See the documentation
CommandTimeout
Gets or sets the wait time (in seconds) before
terminating the attempt to execute a command and generating an error.

C# Connection timeout to oracle database when application pool recycles

We have a web page which uses ODP.Net to connect to oracle database from ASP MVC page. During the heavy user load if application pool recycles for any reason, than we get few connection timeout errors from internal oracle class.
Inner Exception: StackTrace: at OracleInternal.ConnectionPool.PoolManager`3.Get(ConnectionString csWithDiffOrNewPwd, Boolean bGetForApp, String affinityInstanceName, Boolean bForceMatch)
How can we handle this scenario ? what could be the reason for this error ?

If you are using a new connection string that differs per user or with some other variable parameter you can exceed your max connections. Pooling only works if you use the exact same string. Under the covers your "close" is ignored and the connection manager keeps the connection open. In SQL Server you can see a connection reset in the trace console every time an existing connection is reused.
Oracle probably has something similar.
Tracing your connections and possibly connection resets will most likely shed some light on what is creating so many connections.

How to get rid of SqlException Timeout expired in WCF Service?

I'm working on asp.net web application, this application interacts with sql server Database through WCF Service. I get the following Exception sometimes but not every time.
System.Data.SqlClient.SqlException (0x80131904): Timeout expired.
The timeout period elapsed prior to completion of the operation or the server is not responding.
This failure occured while attempting to connect to the Principle server.
---> System.ComponentModel.Win32Exception (0x80004005):
The wait operation timed out
I know there are multiple reasons for this. There's a deadlock somewhere or The query is too complex.
At some place I have read that setting CommandTimeout of SqlCommand object can solve this issue.
So before applying this logic I want to know the strong reason of this issue and If there is any other workaround to be done to get rid of this issue please let me know. If I'm missing anything please let me know.

Connection Timeout Expired. The timeout period elapsed during the post-login phase

In my application, queries are working fine.
For a single select query, i am getting below error.
System.Data.EntityException: The underlying provider failed on Open.
---> System.Data.SqlClient.SqlException: Connection Timeout Expired. The timeout period elapsed during the post-login phase. The
connection could have timed out while waiting for server to complete
the login process and respond; Or it could have timed out while
attempting to create multiple active connections. The duration spent
while attempting to connect to this server was - [Pre-Login]
initialization=0; handshake=13914; [Login] initialization=0;
authentication=0; [Post-Login] complete=1062; --->
System.ComponentModel.Win32Exception: The wait operation timed out
I have ran sqlprofiler for detecting deadlocks but found none.
I am running simple query through entity framework
Any help would be appreciated

Here in stack overflow, there is a post called Help troubleshooting SqlException: Timeout expired on connection, in a non-load situation. It is a problem very similar to your problem. Please take a look.
I will quote (from that post) a comment as a possible cause of your problem:
"Not Enough Memory"
"You may have 'Auto Close' enabled"
"SQL Agent Jobs may be causing problems"
In that post you can see a very good explanation about the topic.

Maybe you forgot to .Close your connection before.
that's why: Or it could have timed out while attempting to create multiple active connections.
(I cant comment for now due to my reputation, dont take this as a full answer)

This looks like a problem with the Active Directory. Maybe a port is blocked (for example 135), so a timeout occurred.

SQLConnection Leakage Issue (Timeout Expired due to Pooling - ASP.NET / SQL Server)

I am developing a web application which is based on ASP.NET 4.0, jQuery, AJAX, Javascript using SQL Server 2008 database. Our application is an ERP application which has almost around 400 to 500 users using the application. We have made it live since a month ago.
Now, I'm facing a timeout issue and application crashed literally which is occurred after some hours of application usage.
Server Error in '/' Application.
--------------------------------------------------------------------------------
Timeout expired. The timeout period elapsed prior to obtaining a connection from the pool. This may have occurred because all pooled connections were in use and max pool size was reached.
Description: An unhandled exception occurred during the execution of the current web request. Please review the stack trace for more information about the error and where it originated in the code.
Exception Details: System.InvalidOperationException: Timeout expired. The timeout period elapsed prior to obtaining a connection from the pool. This may have occurred because all pooled connections were in use and max pool size was reached.
Source Error:
Line 36: param[1].Value = Password;
Line 37:
Line 38: return SqlHelper.ExecuteDataset(CDSGlobal.ConnectionString, CommandType.StoredProcedure, "ValidateLogin_sp", param);
Line 39: }
Line 40:
Source File: e:\abcd\App_Code\User.cs Line: 38
Stack Trace:
[InvalidOperationException: Timeout expired. The timeout period elapsed prior to obtaining a connection from the pool. This may have occurred because all pooled connections were in use and max pool size was reached.]
System.Data.ProviderBase.DbConnectionFactory.GetConnection(DbConnection owningConnection) +6352273
System.Data.ProviderBase.DbConnectionClosed.OpenConnection(DbConnection outerConnection, DbConnectionFactory connectionFactory) +6352606
System.Data.SqlClient.SqlConnection.Open() +300
DBConn.SqlHelper.ExecuteDataset(String connectionString, CommandType commandType, String commandText, SqlParameter[] commandParameters) +270
User.ValidateLogin(String Employee_Code, String Password) in e:\abcd\App_Code \User.cs:38
User_UserLogin.btnLogin_Click(Object sender, EventArgs e) in e:\abcd \User\UserLogin.ascx.cs:79
System.Web.UI.WebControls.Button.RaisePostBackEvent(String eventArgument) +154
System.Web.UI.Page.ProcessRequestMain(Boolean includeStagesBeforeAsyncPoint, Boolean includeStagesAfterAsyncPoint) +3707
--------------------------------------------------------------------------------
Version Information: Microsoft .NET Framework Version:4.0.30319; ASP.NET Version:4.0.30319.272
For temporary resolution, we are restarting the server and restarting the MSSQLSERVER service.
After searching for above, I came to know it is due to connection leakage. Some opened connections are never get closed.
I am using ready made Microsoft Data Access Application Block for .NET i.e. SQLHelper Class which in my application for data access using Dataset and all.
Note: I am NOT using SqlDataReader anywhere.
I have examined the class and its closing the connections and I have NEVER used manual connection code instead used SQLHelper everywhere.
I also have the following nested transactions structure in stored procedures as follows:
BEGIN TRY
BEGIN TRANSACTION
-- Every below stored procedure has the transation structure as this SP i.e. Parent SP. (BEGIN TRY, BEGIN TRANSACTION etc)
exec sp1
exec sp2
exec sp3
---
---
COMMIT TRANSACTION
END TRY
BEGIN CATCH
IF ##TRANCOUNT>0
ROLLBACK TRANSACTION
PRINT 'ERROR OCCURED In SP'
END CATCH
Now, The problem is why connection leakage is occurring.
Is above transaction structure is responsible i.e it is blocking the transactions and requests.
If request is in process and user has closed the browser, does the application closes the connection?
Any help will be greatly appreciated.

Solved !!
It was not due to Nested Transactions but it was due to Bad Indexes Strategy used. Used normal Indexes and Indexes with include to solve the performance issues.
Also ran SQL Profiler to examine the most read and writes on columns and accordingly applied indexes and review maintenance and execution plans. !!

You can also use this,
SqlConnection.ClearAllPools();
The above code then closes all of the pools upon execution. I had the same problem and cleared the pools each time and then it should work successfully due to the pools being cleared.