diff --git a/src/NHibernate.Test/Async/NHSpecificTest/NH2174/Fixture.cs b/src/NHibernate.Test/Async/NHSpecificTest/NH2174/Fixture.cs
index c6fa377a043..77c3127e73f 100644
--- a/src/NHibernate.Test/Async/NHSpecificTest/NH2174/Fixture.cs
+++ b/src/NHibernate.Test/Async/NHSpecificTest/NH2174/Fixture.cs
@@ -25,8 +25,10 @@ protected override void OnSetUp()
 			{
 				var doc = new Document {Id_Base = 1, Id_Doc = 2};
 				session.Save(doc);
-				session.Save(new DocumentDetailDocument {Id_Base = 1, Id_Doc = 2, Id_Item = 1, ReferencedDocument = doc});
+				var detail = new DocumentDetailDocument {Id_Base = 1, Id_Doc = 2, Id_Item = 1, ReferencedDocument = doc};
+				session.Save(detail);
 
+				doc.RefferedDetailsManyToMany.Add(detail);
 				transaction.Commit();
 			}
 		}
@@ -53,6 +55,14 @@ public async Task LinqFetchAsync()
 			}
 		}
 
+		[Test(Description = "GH-3239")]
+		public async Task LinqFetchManyToManyAsync()
+		{
+			using var session = OpenSession();
+			var result = await (session.Query<Document>().Fetch(x => x.RefferedDetailsManyToMany).FirstAsync());
+			Assert.That(result.RefferedDetailsManyToMany, Has.Count.EqualTo(1));
+		}
+
 		[Test]
 		public async Task QueryOverFetchAsync()
 		{
@@ -63,6 +73,14 @@ public async Task QueryOverFetchAsync()
 			}
 		}
 
+		[Test(Description = "GH-3239")]
+		public async Task QueryOverFetchManyToManyAsync()
+		{
+			using var session = OpenSession();
+			var result = await (session.QueryOver<Document>().Fetch(SelectMode.Fetch, x => x.RefferedDetailsManyToMany).SingleOrDefaultAsync());
+			Assert.That(result.RefferedDetailsManyToMany, Has.Count.EqualTo(1));
+		}
+
 		[Test]
 		public async Task LazyLoadAsync()
 		{
@@ -73,5 +91,13 @@ public async Task LazyLoadAsync()
 				Assert.That(result.RefferedDetails.Count, Is.EqualTo(1));
 			}
 		}
+
+		[Test]
+		public async Task LazyLoadManyToManyAsync()
+		{
+			using var session = OpenSession();
+			var result = await (session.Query<Document>().FirstAsync());
+			Assert.That(result.RefferedDetailsManyToMany.Count, Is.EqualTo(1));
+		}
 	}
 }
diff --git a/src/NHibernate.Test/NHSpecificTest/NH2174/Entity.cs b/src/NHibernate.Test/NHSpecificTest/NH2174/Entity.cs
index d3c4702ac69..2b9ea9bfd4f 100644
--- a/src/NHibernate.Test/NHSpecificTest/NH2174/Entity.cs
+++ b/src/NHibernate.Test/NHSpecificTest/NH2174/Entity.cs
@@ -86,6 +86,7 @@ public override int GetHashCode()
 		private int _id_Doc;
 		private int _id_base;
 		public virtual IList<DocumentDetailDocument> RefferedDetails { get; set; } = new List<DocumentDetailDocument>();
+		public virtual IList<DocumentDetailDocument> RefferedDetailsManyToMany { get; set; } = new List<DocumentDetailDocument>();
 
 		public int Id_Doc
 		{
diff --git a/src/NHibernate.Test/NHSpecificTest/NH2174/Fixture.cs b/src/NHibernate.Test/NHSpecificTest/NH2174/Fixture.cs
index 13d9922c9d2..a216a4d2357 100644
--- a/src/NHibernate.Test/NHSpecificTest/NH2174/Fixture.cs
+++ b/src/NHibernate.Test/NHSpecificTest/NH2174/Fixture.cs
@@ -14,8 +14,10 @@ protected override void OnSetUp()
 			{
 				var doc = new Document {Id_Base = 1, Id_Doc = 2};
 				session.Save(doc);
-				session.Save(new DocumentDetailDocument {Id_Base = 1, Id_Doc = 2, Id_Item = 1, ReferencedDocument = doc});
+				var detail = new DocumentDetailDocument {Id_Base = 1, Id_Doc = 2, Id_Item = 1, ReferencedDocument = doc};
+				session.Save(detail);
 
+				doc.RefferedDetailsManyToMany.Add(detail);
 				transaction.Commit();
 			}
 		}
@@ -42,6 +44,14 @@ public void LinqFetch()
 			}
 		}
 
+		[Test(Description = "GH-3239")]
+		public void LinqFetchManyToMany()
+		{
+			using var session = OpenSession();
+			var result = session.Query<Document>().Fetch(x => x.RefferedDetailsManyToMany).First();
+			Assert.That(result.RefferedDetailsManyToMany, Has.Count.EqualTo(1));
+		}
+
 		[Test]
 		public void QueryOverFetch()
 		{
@@ -52,6 +62,14 @@ public void QueryOverFetch()
 			}
 		}
 
+		[Test(Description = "GH-3239")]
+		public void QueryOverFetchManyToMany()
+		{
+			using var session = OpenSession();
+			var result = session.QueryOver<Document>().Fetch(SelectMode.Fetch, x => x.RefferedDetailsManyToMany).SingleOrDefault();
+			Assert.That(result.RefferedDetailsManyToMany, Has.Count.EqualTo(1));
+		}
+
 		[Test]
 		public void LazyLoad()
 		{
@@ -62,5 +80,13 @@ public void LazyLoad()
 				Assert.That(result.RefferedDetails.Count, Is.EqualTo(1));
 			}
 		}
+
+		[Test]
+		public void LazyLoadManyToMany()
+		{
+			using var session = OpenSession();
+			var result = session.Query<Document>().First();
+			Assert.That(result.RefferedDetailsManyToMany.Count, Is.EqualTo(1));
+		}
 	}
 }
diff --git a/src/NHibernate.Test/NHSpecificTest/NH2174/Mappings.hbm.xml b/src/NHibernate.Test/NHSpecificTest/NH2174/Mappings.hbm.xml
index b6b056c2f80..d04459f0265 100644
--- a/src/NHibernate.Test/NHSpecificTest/NH2174/Mappings.hbm.xml
+++ b/src/NHibernate.Test/NHSpecificTest/NH2174/Mappings.hbm.xml
@@ -42,5 +42,18 @@
       </key>
       <one-to-many class="DocumentDetailDocument" />
     </bag>
+    
+    <bag name="RefferedDetailsManyToMany" lazy="true" generic="true" cascade="all">
+      <key>
+        <column name="id_Doc_detail" />
+        <column name="id_base_detail" />
+      </key>
+      <many-to-many class="DocumentDetailDocument" >
+        <column name="id_item" />
+        <column name="Version" />
+        <column name="id_Doc" />
+        <column name="id_base" />
+      </many-to-many>
+    </bag>
   </class>
 </hibernate-mapping>
diff --git a/src/NHibernate/Engine/TableGroupJoinHelper.cs b/src/NHibernate/Engine/TableGroupJoinHelper.cs
index 18dddb12dfe..12ad3be28a2 100644
--- a/src/NHibernate/Engine/TableGroupJoinHelper.cs
+++ b/src/NHibernate/Engine/TableGroupJoinHelper.cs
@@ -68,15 +68,18 @@ private static bool NeedsTableGroupJoin(IReadOnlyList<IJoin> joins, SqlString[]
 
 			foreach (var join in joins)
 			{
-				var entityPersister = GetEntityPersister(join.Joinable);
+				var entityPersister = GetEntityPersister(join.Joinable, out var isManyToMany);
 				if (entityPersister?.HasSubclassJoins(includeSubclasses && isSubclassIncluded(join.Alias)) != true)
 					continue;
 
 				if (hasWithClause)
 					return true;
 
-				if (entityPersister.ColumnsDependOnSubclassJoins(join.RHSColumns))
+				if (!isManyToMany // many-to-many keys are stored in separate table
+				    && entityPersister.ColumnsDependOnSubclassJoins(join.RHSColumns))
+				{
 					return true;
+				}
 			}
 
 			return false;
@@ -91,14 +94,16 @@ private static SqlString GetTableGroupJoinWithClause(SqlString[] withClauseFragm
 			var isAssociationJoin = lhsColumns.Length > 0;
 			if (isAssociationJoin)
 			{
-				var entityPersister = GetEntityPersister(first.Joinable);
+				var entityPersister = GetEntityPersister(first.Joinable, out var isManyToMany);
 				string rhsAlias = first.Alias;
 				string[] rhsColumns = first.RHSColumns;
 				for (int j = 0; j < lhsColumns.Length; j++)
 				{
 					fromFragment.Add(lhsColumns[j])
 								.Add("=")
-								.Add(entityPersister?.GenerateTableAliasForColumn(rhsAlias, rhsColumns[j]) ?? rhsAlias)
+								.Add((entityPersister == null || isManyToMany) // many-to-many keys are stored in separate table
+									     ? rhsAlias
+									     : entityPersister.GenerateTableAliasForColumn(rhsAlias, rhsColumns[j]))
 								.Add(".")
 								.Add(rhsColumns[j]);
 					if (j != lhsColumns.Length - 1)
@@ -111,12 +116,14 @@ private static SqlString GetTableGroupJoinWithClause(SqlString[] withClauseFragm
 			return fromFragment.ToSqlString();
 		}
 
-		private static AbstractEntityPersister GetEntityPersister(IJoinable joinable)
+		private static AbstractEntityPersister GetEntityPersister(IJoinable joinable, out bool isManyToMany)
 		{
+			isManyToMany = false;
 			if (!joinable.IsCollection)
 				return joinable as AbstractEntityPersister;
 
 			var collection = (IQueryableCollection) joinable;
+			isManyToMany = collection.IsManyToMany;
 			return collection.ElementType.IsEntityType ? collection.ElementPersister as AbstractEntityPersister : null;
 		}