Index: Riskeer/Integration/src/Riskeer.Integration.Plugin/Merge/AssessmentSectionMergeHandler.cs
===================================================================
diff -u -r6bb3c5039c95b9056e5ec7c293a5b3f31eddf986 -r95ef54e2348b92a2b9c0c7d0737e2508f8fc3ac4
--- Riskeer/Integration/src/Riskeer.Integration.Plugin/Merge/AssessmentSectionMergeHandler.cs	(.../AssessmentSectionMergeHandler.cs)	(revision 6bb3c5039c95b9056e5ec7c293a5b3f31eddf986)
+++ Riskeer/Integration/src/Riskeer.Integration.Plugin/Merge/AssessmentSectionMergeHandler.cs	(.../AssessmentSectionMergeHandler.cs)	(revision 95ef54e2348b92a2b9c0c7d0737e2508f8fc3ac4)
@@ -95,7 +95,6 @@
                                                                                sourceAssessmentSection.WaterLevelCalculationsForLowerLimitNorm));
             changedObjects.AddRange(MergeHydraulicBoundaryLocationCalculations(targetAssessmentSection.WaterLevelCalculationsForFactorizedLowerLimitNorm,
                                                                                sourceAssessmentSection.WaterLevelCalculationsForFactorizedLowerLimitNorm));
-
             changedObjects.AddRange(MergeHydraulicBoundaryLocationCalculations(targetAssessmentSection.WaveHeightCalculationsForFactorizedSignalingNorm,
                                                                                sourceAssessmentSection.WaveHeightCalculationsForFactorizedSignalingNorm));
             changedObjects.AddRange(MergeHydraulicBoundaryLocationCalculations(targetAssessmentSection.WaveHeightCalculationsForSignalingNorm,
@@ -105,13 +104,48 @@
             changedObjects.AddRange(MergeHydraulicBoundaryLocationCalculations(targetAssessmentSection.WaveHeightCalculationsForFactorizedLowerLimitNorm,
                                                                                sourceAssessmentSection.WaveHeightCalculationsForFactorizedLowerLimitNorm));
 
+            ObservableList<HydraulicBoundaryLocationCalculationsForTargetProbability> sourceProbabilities = sourceAssessmentSection.WaterLevelCalculationsForUserDefinedTargetProbabilities;
+
+            HydraulicBoundaryLocationCalculationsForTargetProbability[] probabilitiesToMerge = sourceAssessmentSection.WaterLevelCalculationsForUserDefinedTargetProbabilities
+                                                                                                                      .Where(sp => targetAssessmentSection.WaterLevelCalculationsForUserDefinedTargetProbabilities
+                                                                                                                                                          .Select(c => c.TargetProbability)
+                                                                                                                                                          .Contains(sp.TargetProbability)).ToArray();
+
+            foreach (HydraulicBoundaryLocationCalculationsForTargetProbability sourceProbability in probabilitiesToMerge)
+            {
+                HydraulicBoundaryLocationCalculationsForTargetProbability targetProbability = targetAssessmentSection.WaterLevelCalculationsForUserDefinedTargetProbabilities.First(c => c.TargetProbability.Equals(sourceProbability.TargetProbability));
+
+                changedObjects.AddRange(MergeHydraulicBoundaryLocationCalculations(targetProbability.HydraulicBoundaryLocationCalculations, sourceProbability.HydraulicBoundaryLocationCalculations));
+            }
+
+            IEnumerable<HydraulicBoundaryLocationCalculationsForTargetProbability> targetProbabilities = sourceProbabilities.Except(probabilitiesToMerge);
+
+            MergeUniqueProbabilities(targetAssessmentSection, targetProbabilities);
+
             log.Info(changedObjects.Any()
                          ? Resources.AssessmentSectionMergeHandler_MergeHydraulicBoundaryLocations_HydraulicBoundaryLocations_merged
                          : Resources.AssessmentSectionMergeHandler_MergeHydraulicBoundaryLocations_HydraulicBoundaryLocations_not_merged);
 
             return changedObjects;
         }
 
+        private static void MergeUniqueProbabilities(IAssessmentSection targetAssessmentSection, IEnumerable<HydraulicBoundaryLocationCalculationsForTargetProbability> targetProbabilities)
+        {
+            foreach (HydraulicBoundaryLocationCalculationsForTargetProbability targetProbability in targetProbabilities)
+            {
+                var newTargetProbability = new HydraulicBoundaryLocationCalculationsForTargetProbability
+                {
+                    TargetProbability = targetProbability.TargetProbability
+                };
+
+                newTargetProbability.HydraulicBoundaryLocationCalculations.AddRange(targetProbability.HydraulicBoundaryLocationCalculations
+                                                                                                     .Select(calculation => new HydraulicBoundaryLocationCalculation(GetHydraulicBoundaryLocation(calculation.HydraulicBoundaryLocation, targetAssessmentSection.HydraulicBoundaryDatabase.Locations)))
+                                                                                                     .ToArray());
+
+                targetAssessmentSection.WaterLevelCalculationsForUserDefinedTargetProbabilities.Add(newTargetProbability);
+            }
+        }
+
         private static IEnumerable<IObservable> MergeHydraulicBoundaryLocationCalculations(IEnumerable<HydraulicBoundaryLocationCalculation> targetCalculations,
                                                                                            IEnumerable<HydraulicBoundaryLocationCalculation> sourceCalculations)
         {
Index: Riskeer/Integration/test/Riskeer.Integration.Plugin.Test/Merge/AssessmentSectionMergeHandlerTest.cs
===================================================================
diff -u -r3e0814af5f0045f57ab89723d8d55db530c8f6f5 -r95ef54e2348b92a2b9c0c7d0737e2508f8fc3ac4
--- Riskeer/Integration/test/Riskeer.Integration.Plugin.Test/Merge/AssessmentSectionMergeHandlerTest.cs	(.../AssessmentSectionMergeHandlerTest.cs)	(revision 3e0814af5f0045f57ab89723d8d55db530c8f6f5)
+++ Riskeer/Integration/test/Riskeer.Integration.Plugin.Test/Merge/AssessmentSectionMergeHandlerTest.cs	(.../AssessmentSectionMergeHandlerTest.cs)	(revision 95ef54e2348b92a2b9c0c7d0737e2508f8fc3ac4)
@@ -395,6 +395,95 @@
                                                 targetLocations);
         }
 
+        [Test]
+        public void GivenEqualUserDefinedTargetProbabilities_WhenMerging_ThenCalculationsMerged()
+        {
+            // Given
+            var handler = new AssessmentSectionMergeHandler();
+
+            var targetLocations = new[]
+            {
+                new HydraulicBoundaryLocation(1, "location 1", 1, 1),
+                new HydraulicBoundaryLocation(2, "location 2", 2, 2)
+            };
+
+            var sourceLocations = new[]
+            {
+                new HydraulicBoundaryLocation(1, "location 1", 1, 1),
+                new HydraulicBoundaryLocation(2, "location 2", 2, 2)
+            };
+
+            AssessmentSection targetAssessmentSection = CreateAssessmentSection(targetLocations);
+            AssessmentSection sourceAssessmentSection = CreateAssessmentSection(sourceLocations);
+
+            // When
+            handler.PerformMerge(targetAssessmentSection, new AssessmentSectionMergeData(
+                                     sourceAssessmentSection,
+                                     new AssessmentSectionMergeData.ConstructionProperties
+                                     {
+                                         MergePiping = false,
+                                         MergeGrassCoverErosionInwards = false,
+                                         MergeMacroStabilityInwards = false,
+                                         MergeStabilityStoneCover = false,
+                                         MergeWaveImpactAsphaltCover = false,
+                                         MergeGrassCoverErosionOutwards = false,
+                                         MergeHeightStructures = false,
+                                         MergeClosingStructures = false,
+                                         MergeStabilityPointStructures = false
+                                     }));
+
+            // Then
+            foreach (HydraulicBoundaryLocationCalculationsForTargetProbability tp in sourceAssessmentSection.WaterLevelCalculationsForUserDefinedTargetProbabilities)
+            {
+                HydraulicBoundaryLocationCalculationsForTargetProbability targetProbability = targetAssessmentSection.WaterLevelCalculationsForUserDefinedTargetProbabilities.First(c => c.TargetProbability.Equals(tp.TargetProbability));
+
+                AssertHydraulicBoundaryCalculations(tp.HydraulicBoundaryLocationCalculations, targetProbability.HydraulicBoundaryLocationCalculations, targetLocations);
+            }
+        }
+
+        [Test]
+        public void GivenDifferentUserDefinedTargetProbabilities_WhenMerging_ThenCalculationsMerged()
+        {
+            // Given
+            var handler = new AssessmentSectionMergeHandler();
+
+            var targetLocations = new[]
+            {
+                new HydraulicBoundaryLocation(1, "location 1", 1, 1),
+                new HydraulicBoundaryLocation(2, "location 2", 2, 2)
+            };
+
+            var sourceLocations = new[]
+            {
+                new HydraulicBoundaryLocation(1, "location 1", 1, 1),
+                new HydraulicBoundaryLocation(2, "location 2", 2, 2)
+            };
+
+            AssessmentSection targetAssessmentSection = CreateAssessmentSection(targetLocations);
+            AssessmentSection sourceAssessmentSection = CreateAssessmentSection(sourceLocations);
+
+            sourceAssessmentSection.WaterLevelCalculationsForUserDefinedTargetProbabilities[0].TargetProbability = 0.01;
+
+            // When
+            handler.PerformMerge(targetAssessmentSection, new AssessmentSectionMergeData(
+                                     sourceAssessmentSection,
+                                     new AssessmentSectionMergeData.ConstructionProperties
+                                     {
+                                         MergePiping = false,
+                                         MergeGrassCoverErosionInwards = false,
+                                         MergeMacroStabilityInwards = false,
+                                         MergeStabilityStoneCover = false,
+                                         MergeWaveImpactAsphaltCover = false,
+                                         MergeGrassCoverErosionOutwards = false,
+                                         MergeHeightStructures = false,
+                                         MergeClosingStructures = false,
+                                         MergeStabilityPointStructures = false
+                                     }));
+
+            // Then
+            Assert.AreEqual(targetAssessmentSection.WaterLevelCalculationsForUserDefinedTargetProbabilities.Count(c => c.TargetProbability.Equals(0.01)), 1);
+        }
+
         private static void AssertHydraulicBoundaryCalculations(IEnumerable<HydraulicBoundaryLocationCalculation> sourceCalculations,
                                                                 IEnumerable<HydraulicBoundaryLocationCalculation> targetCalculations,
                                                                 IEnumerable<HydraulicBoundaryLocation> targetLocations)
@@ -416,6 +505,21 @@
         private static AssessmentSection CreateAssessmentSection(HydraulicBoundaryLocation[] locations)
         {
             var assessmentSection = new AssessmentSection(AssessmentSectionComposition.Dike);
+            assessmentSection.WaterLevelCalculationsForUserDefinedTargetProbabilities.Add(new HydraulicBoundaryLocationCalculationsForTargetProbability
+            {
+                HydraulicBoundaryLocationCalculations =
+                {
+                    new HydraulicBoundaryLocationCalculation(locations[0])
+                }
+            });
+
+            assessmentSection.WaveHeightCalculationsForUserDefinedTargetProbabilities.Add(new HydraulicBoundaryLocationCalculationsForTargetProbability
+            {
+                HydraulicBoundaryLocationCalculations =
+                {
+                    new HydraulicBoundaryLocationCalculation(locations[1])
+                }
+            });
             assessmentSection.HydraulicBoundaryDatabase.Locations.AddRange(locations);
             assessmentSection.SetHydraulicBoundaryLocationCalculations(locations);
             return assessmentSection;