diff --git a/ApplicationLibCode/ProjectDataModel/RimDockWindowController.cpp b/ApplicationLibCode/ProjectDataModel/RimDockWindowController.cpp
index e20b239603..24a594baa4 100644
--- a/ApplicationLibCode/ProjectDataModel/RimDockWindowController.cpp
+++ b/ApplicationLibCode/ProjectDataModel/RimDockWindowController.cpp
@@ -217,16 +217,32 @@ void RimDockWindowController::setAsActiveViewer( bool allowSelectionChange )
         auto view3d   = dynamic_cast<Rim3dView*>( pdmView );
         auto viewPlot = dynamic_cast<RimPlotWindow*>( pdmView );
 
-        RiuMainWindowBase* mainWindow = RiaGuiApplication::instance()->mainWindow();
-        if ( viewPlot ) mainWindow = RiaGuiApplication::instance()->mainPlotWindow();
-        if ( !mainWindow ) return;
+        auto app = RiaGuiApplication::instance();
 
-        for ( auto view : mainWindow->viewWindows() )
+        auto deactivate = []( RimViewWindow* view )
         {
-            if ( view->isActiveViewer() )
+            if ( !view->isActiveViewer() ) return;
+            view->setActive( false );
+            view->updateWindowTitle();
+        };
+
+        // The active 3D view and the active plot are tracked separately
+        if ( auto project = RimProject::current() )
+        {
+            if ( view3d )
             {
-                view->setActive( false );
-                view->updateWindowTitle();
+                // Search the project, as a 3D view can be docked in both the 3D window and the plot window
+                for ( auto view : project->descendantsOfType<Rim3dView>() )
+                {
+                    deactivate( view );
+                }
+            }
+            else
+            {
+                for ( auto view : project->descendantsOfType<RimViewWindow>() )
+                {
+                    if ( !dynamic_cast<Rim3dView*>( view ) ) deactivate( view );
+                }
             }
         }
 
@@ -235,8 +251,11 @@ void RimDockWindowController::setAsActiveViewer( bool allowSelectionChange )
 
         if ( view3d )
         {
-            RiaApplication::instance()->setActiveReservoirView( view3d );
-            if ( auto mainWin = dynamic_cast<RiuMainWindow*>( mainWindow ) )
+            app->setActiveReservoirView( view3d );
+
+            // The toolbars controlling 3D views (e.g. time step animation) are only available in the 3D main window, also
+            // for 3D views docked in the plot window
+            if ( auto mainWin = app->mainWindow() )
             {
                 mainWin->refreshViewActions();
                 mainWin->refreshAnimationActions();
diff --git a/ApplicationLibCode/UserInterface/RiuMainWindow.cpp b/ApplicationLibCode/UserInterface/RiuMainWindow.cpp
index 95f7ace8d9..122d3ee8c2 100644
--- a/ApplicationLibCode/UserInterface/RiuMainWindow.cpp
+++ b/ApplicationLibCode/UserInterface/RiuMainWindow.cpp
@@ -64,6 +64,7 @@
 #include "RiuMenuBarBuildTools.h"
 #include "RiuMessagePanel.h"
 #include "RiuMohrsCirclePlot.h"
+#include "RiuPlotMainWindow.h"
 #include "RiuProcessMonitor.h"
 #include "RiuProjectPropertyView.h"
 #include "RiuPropertyViewTabWidget.h"
@@ -1285,9 +1286,10 @@ std::vector<RimViewWindow*> RiuMainWindow::viewWindows()
     // Project can be null while it is being torn down.
     if ( auto project = RimProject::current() )
     {
+        // 3D views docked in the plot window are handled by RiuPlotMainWindow
         for ( auto v : project->descendantsOfType<Rim3dView>() )
         {
-            if ( v->dockWidget() ) views.push_back( v );
+            if ( v->dockWidget() && !v->isDockedInPlotView() ) views.push_back( v );
         }
     }
 
@@ -2326,6 +2328,31 @@ RimViewWindow* RiuMainWindow::activeViewer()
     return RiaApplication::instance()->activeReservoirView();
 }
 
+//--------------------------------------------------------------------------------------------------
+///
+//--------------------------------------------------------------------------------------------------
+void RiuMainWindow::setActiveViewer( QString viewerName )
+{
+    // 3D views docked in the plot window are managed by the plot main window
+    auto plotWindow = RiaGuiApplication::instance()->mainPlotWindow();
+    if ( auto project = RimProject::current(); project && plotWindow )
+    {
+        for ( auto view : project->descendantsOfType<Rim3dView>() )
+        {
+            if ( view->isDockedInPlotView() && view->dockWindowName() == viewerName )
+            {
+                const bool wasBlocking = plotWindow->isBlockingViewSelectionOnSubWindowActivated();
+                plotWindow->setBlockViewSelectionOnSubWindowActivated( isBlockingViewSelectionOnSubWindowActivated() );
+                plotWindow->setActiveViewer( viewerName );
+                plotWindow->setBlockViewSelectionOnSubWindowActivated( wasBlocking );
+                return;
+            }
+        }
+    }
+
+    RiuMainWindowBase::setActiveViewer( viewerName );
+}
+
 //--------------------------------------------------------------------------------------------------
 ///
 //--------------------------------------------------------------------------------------------------
diff --git a/ApplicationLibCode/UserInterface/RiuMainWindow.h b/ApplicationLibCode/UserInterface/RiuMainWindow.h
index f545a90ce3..6a838d2dc2 100644
--- a/ApplicationLibCode/UserInterface/RiuMainWindow.h
+++ b/ApplicationLibCode/UserInterface/RiuMainWindow.h
@@ -101,6 +101,7 @@ class RiuMainWindow : public RiuMainWindowBase
     void           onViewerRemoved() override;
     void           initializeViewer( ads::CDockWidget* dockWidget, QWidget* viewer ) override;
     RimViewWindow* activeViewer() override;
+    void           setActiveViewer( QString viewerName ) override;
 
     std::vector<RimViewWindow*> viewWindows() override;
 
diff --git a/ApplicationLibCode/UserInterface/RiuPlotMainWindow.cpp b/ApplicationLibCode/UserInterface/RiuPlotMainWindow.cpp
index 6d7b1f325e..f950b8ccf1 100644
--- a/ApplicationLibCode/UserInterface/RiuPlotMainWindow.cpp
+++ b/ApplicationLibCode/UserInterface/RiuPlotMainWindow.cpp
@@ -860,9 +860,12 @@ std::vector<RimViewWindow*> RiuPlotMainWindow::viewWindows()
     // Project can be null while it is being torn down.
     if ( auto project = RimProject::current() )
     {
-        for ( auto v : project->descendantsOfType<RimPlotWindow>() )
+        // Some plots (e.g. flow diagnostics plots) derive directly from RimViewWindow, and are identified by being docked in the plot
+        // window
+        for ( auto v : project->descendantsOfType<RimViewWindow>() )
         {
-            if ( v->dockWidget() ) views.push_back( v );
+            if ( !v->dockWidget() ) continue;
+            if ( dynamic_cast<RimPlotWindow*>( v ) || v->isDockedInPlotView() ) views.push_back( v );
         }
     }
 
diff --git a/ApplicationLibCode/UserInterface/RiuPlotMainWindowTools.cpp b/ApplicationLibCode/UserInterface/RiuPlotMainWindowTools.cpp
index 588a30cda7..895c93de8e 100644
--- a/ApplicationLibCode/UserInterface/RiuPlotMainWindowTools.cpp
+++ b/ApplicationLibCode/UserInterface/RiuPlotMainWindowTools.cpp
@@ -20,6 +20,7 @@
 
 #include "RiaGuiApplication.h"
 
+#include "Rim3dView.h"
 #include "RimViewWindow.h"
 
 #include "RiuMainWindow.h"
@@ -169,11 +170,11 @@ void RiuPlotMainWindowTools::remove3dViewsFromDocking()
 {
     if ( !RiaGuiApplication::isRunning() ) return;
 
-    if ( auto mainWnd = RiaGuiApplication::instance()->mainWindow() )
+    if ( auto plotWnd = RiaGuiApplication::instance()->mainPlotWindow() )
     {
-        for ( auto view : mainWnd->viewWindows() )
+        for ( auto view : plotWnd->viewWindows() )
         {
-            if ( view->isDockedInPlotView() )
+            if ( dynamic_cast<Rim3dView*>( view ) && view->isDockedInPlotView() )
             {
                 view->setShowWindow( false );
                 view->removeWindowFromDock();