diff --git a/main/settings/src/main/scala/sbt/Reference.scala b/main/settings/src/main/scala/sbt/Reference.scala
index 21d1b195e..f970d5eb2 100644
--- a/main/settings/src/main/scala/sbt/Reference.scala
+++ b/main/settings/src/main/scala/sbt/Reference.scala
@@ -98,7 +98,13 @@ object Reference
 		case BuildRef(b) => Some(b)
 		case _ => None
 	}
+
+	@deprecated("Explicitly wrap the URI in a call to RootProject.", "0.13.0")
 	implicit def uriToRef(u: URI): ProjectReference = RootProject(u)
+
+	@deprecated("Explicitly wrap the File in a call to RootProject.", "0.13.0")
 	implicit def fileToRef(f: File): ProjectReference = RootProject(f)
+
+	@deprecated("Explicitly wrap the String in a call to LocalProject.", "0.13.0")
 	implicit def stringToReference(s: String): ProjectReference = LocalProject(s)
 }
\ No newline at end of file