The low-level answer here is that a Web Reference will create a client proxy class that allows your code to talk to a Web Service that is described via WSDL and communicates via SOAP or HTTP GET (other posters indicate that it is only ASMX, but Web References can also talk to Java-based Web Services or Python-based or Ruby so long as they all talk WSDL and conform to the WS-I interoperability standard).
A Service Reference will create a client proxy class that communicates with a WCF-based service : regardless of whether that WCF service is a Web Service or not.
A Web Reference allows you to communicate with any service based on any technology that implements the WS-I Basic Profile 1.1, and exposes the relevant metadata as WSDL. Internally, it uses the ASMX communication stack on the client's side.
A Service Reference allows you to communicate with any service based on any technology that implements any of the many protocols supported by WCF (including but not limited to WS-I Basic Profile). Internally, it uses the WCF communication stack on the client side.
Note that both these definitions are quite wide, and both include services not written in .NET.
It is perfectly possible (though not recommended) to add a Web Reference that points to a WCF service, as long as the WCF endpoint uses basicHttpBinding
or some compatible custom variant.
It is also possible to add a Service Reference that points to an ASMX service. When writing new code, you should always use a Service Reference simply because it is more flexible and future-proof.
The service reference is the newer interface for adding references to all manner of WCF services (they may not be web services) whereas Web reference is specifically concerned with ASMX web references.
You can access web references via the advanced options in add service reference (if I recall correctly).
I'd use service reference because as I understand it, it's the newer mechanism of the two.
Service references deal with endpoints and bindings, which are completely configurable. They let you point your client proxy to a WCF via any transport protocol (HTTP, TCP, Shared Memory, etc)
They are designed to work with WCF.
If you use a WebProxy, you are pretty much binding yourself to using WCF over HTTP
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