diff --git a/gdk/wayland/gdkdevice-wayland.c b/gdk/wayland/gdkdevice-wayland.c
index d00524f048..d5ac46e1b0 100644
--- a/gdk/wayland/gdkdevice-wayland.c
+++ b/gdk/wayland/gdkdevice-wayland.c
@@ -584,15 +584,18 @@ gdk_wayland_device_query_state (GdkDevice        *device,
                                 GdkModifierType  *mask)
 {
   GdkWaylandPointerData *pointer;
+  GList *children;
 
   if (window == NULL)
-    window = GDK_WAYLAND_DISPLAY (gdk_device_get_display (device))->root_window;
+    children = gdk_wayland_display_get_toplevel_windows (gdk_device_get_display (device));
+  else
+    children = window->children;
 
   pointer = GDK_WAYLAND_DEVICE (device)->pointer;
 
   if (child_window)
     /* Set child only if actually a child of the given window, as XIQueryPointer() does */
-    *child_window = g_list_find (window->children, pointer->focus) ? pointer->focus : NULL;
+    *child_window = g_list_find (children, pointer->focus) ? pointer->focus : NULL;
   if (mask)
     *mask = device_get_modifiers (device);
 
diff --git a/gdk/wayland/gdkdisplay-wayland.c b/gdk/wayland/gdkdisplay-wayland.c
index 9cfebacad0..f74dd2ad79 100644
--- a/gdk/wayland/gdkdisplay-wayland.c
+++ b/gdk/wayland/gdkdisplay-wayland.c
@@ -600,7 +600,6 @@ _gdk_wayland_display_open (const gchar *display_name)
 
   display_wayland = GDK_WAYLAND_DISPLAY (display);
   display_wayland->wl_display = wl_display;
-  display_wayland->root_window = _gdk_wayland_display_create_root_window (display, 0, 0);
   display_wayland->event_source = _gdk_wayland_display_event_source_new (display);
 
   init_settings (display);
@@ -644,13 +643,18 @@ _gdk_wayland_display_open (const gchar *display_name)
   return display;
 }
 
+static void
+destroy_toplevel (gpointer data)
+{
+  _gdk_window_destroy (GDK_WINDOW (data), FALSE);
+}
+
 static void
 gdk_wayland_display_dispose (GObject *object)
 {
   GdkWaylandDisplay *display_wayland = GDK_WAYLAND_DISPLAY (object);
 
-  if (display_wayland->root_window)
-    _gdk_window_destroy (display_wayland->root_window, FALSE);
+  g_list_free_full (display_wayland->toplevels, destroy_toplevel);
 
   if (display_wayland->event_source)
     {
@@ -686,9 +690,6 @@ gdk_wayland_display_finalize (GObject *object)
 
   _gdk_wayland_display_finalize_cursors (display_wayland);
 
-  if (display_wayland->root_window)
-    g_object_unref (display_wayland->root_window);
-
   g_free (display_wayland->startup_notification_id);
   g_free (display_wayland->cursor_theme_name);
   xkb_context_unref (display_wayland->xkb_context);
@@ -1062,6 +1063,12 @@ gdk_wayland_display_init (GdkWaylandDisplay *display)
   display->monitors = g_ptr_array_new_with_free_func (g_object_unref);
 }
 
+GList *
+gdk_wayland_display_get_toplevel_windows (GdkDisplay *display)
+{
+  return GDK_WAYLAND_DISPLAY (display)->toplevels;
+}
+
 void
 gdk_wayland_display_set_cursor_theme (GdkDisplay  *display,
                                       const gchar *name,
@@ -1899,6 +1906,14 @@ transform_to_string (int transform)
 
 #endif
 
+static void
+update_scale (GdkDisplay *display)
+{
+  g_list_foreach (gdk_wayland_display_get_toplevel_windows (display),
+                  (GFunc)gdk_wayland_window_update_scale,
+                  NULL);
+}
+
 static void
 output_handle_geometry (void             *data,
                         struct wl_output *wl_output,
@@ -1924,10 +1939,7 @@ output_handle_geometry (void             *data,
   gdk_monitor_set_model (GDK_MONITOR (monitor), model);
 
   if (GDK_MONITOR (monitor)->geometry.width != 0 && monitor->version < OUTPUT_VERSION_WITH_DONE)
-    {
-      GdkDisplay *display = GDK_MONITOR (monitor)->display;
-      window_update_scale (GDK_WAYLAND_DISPLAY (display)->root_window);
-    }
+    update_scale (GDK_MONITOR (monitor)->display);
 }
 
 static void
@@ -1947,7 +1959,7 @@ output_handle_done (void             *data,
       gdk_display_monitor_added (display, GDK_MONITOR (monitor));
     }
 
-  window_update_scale (GDK_WAYLAND_DISPLAY (display)->root_window);
+  update_scale (display);
 }
 
 static void
@@ -1974,7 +1986,7 @@ output_handle_scale (void             *data,
   gdk_monitor_set_size (GDK_MONITOR (monitor), width / scale, height / scale);
 
   if (GDK_MONITOR (monitor)->geometry.width != 0 && monitor->version < OUTPUT_VERSION_WITH_DONE)
-    window_update_scale (GDK_WAYLAND_DISPLAY (GDK_MONITOR (monitor)->display)->root_window);
+    update_scale (GDK_MONITOR (monitor)->display);
 }
 
 static void
@@ -2000,7 +2012,7 @@ output_handle_mode (void             *data,
   gdk_monitor_set_refresh_rate (GDK_MONITOR (monitor), refresh);
 
   if (width != 0 && monitor->version < OUTPUT_VERSION_WITH_DONE)
-    window_update_scale (GDK_WAYLAND_DISPLAY (GDK_MONITOR (monitor)->display)->root_window);
+    update_scale (GDK_MONITOR (monitor)->display);
 }
 
 static const struct wl_output_listener output_listener =
@@ -2093,7 +2105,7 @@ gdk_wayland_display_remove_output (GdkWaylandDisplay *display_wayland,
       g_object_ref (monitor);
       g_ptr_array_remove (display_wayland->monitors, monitor);
       gdk_display_monitor_removed (GDK_DISPLAY (display_wayland), GDK_MONITOR (monitor));
-      window_update_scale (display_wayland->root_window);
+      update_scale (GDK_DISPLAY (display_wayland));
       g_object_unref (monitor);
     }
 }
diff --git a/gdk/wayland/gdkdisplay-wayland.h b/gdk/wayland/gdkdisplay-wayland.h
index ed59818590..c38c810153 100644
--- a/gdk/wayland/gdkdisplay-wayland.h
+++ b/gdk/wayland/gdkdisplay-wayland.h
@@ -64,7 +64,7 @@ typedef struct {
 struct _GdkWaylandDisplay
 {
   GdkDisplay parent_instance;
-  GdkWindow *root_window;
+  GList *toplevels;
 
   GHashTable *settings;
   GsdXftSettings xft_settings;
diff --git a/gdk/wayland/gdkprivate-wayland.h b/gdk/wayland/gdkprivate-wayland.h
index 223b963b48..98789d6ae3 100644
--- a/gdk/wayland/gdkprivate-wayland.h
+++ b/gdk/wayland/gdkprivate-wayland.h
@@ -199,6 +199,8 @@ GdkWindow *_gdk_wayland_display_create_root_window (GdkDisplay *display,
                                                     int         width,
                                                     int         height);
 
+GList *gdk_wayland_display_get_toplevel_windows (GdkDisplay *display);
+
 int gdk_wayland_display_get_output_refresh_rate (GdkWaylandDisplay *display_wayland,
                                                  struct wl_output  *output);
 guint32 gdk_wayland_display_get_output_scale (GdkWaylandDisplay *display_wayland,
@@ -265,7 +267,7 @@ void gdk_wayland_window_inhibit_shortcuts (GdkWindow *window,
 void gdk_wayland_window_restore_shortcuts (GdkWindow *window,
                                            GdkSeat   *gdk_seat);
 
-void window_update_scale (GdkWindow *window);
+void gdk_wayland_window_update_scale (GdkWindow *window);
 
 
 #endif /* __GDK_PRIVATE_WAYLAND_H__ */
diff --git a/gdk/wayland/gdkwindow-wayland.c b/gdk/wayland/gdkwindow-wayland.c
index 03396528ed..235c4e97c5 100644
--- a/gdk/wayland/gdkwindow-wayland.c
+++ b/gdk/wayland/gdkwindow-wayland.c
@@ -610,7 +610,7 @@ on_frame_clock_after_paint (GdkFrameClock *clock,
 }
 
 void
-window_update_scale (GdkWindow *window)
+gdk_wayland_window_update_scale (GdkWindow *window)
 {
   GdkWindowImplWayland *impl = GDK_WINDOW_IMPL_WAYLAND (window->impl);
   GdkWaylandDisplay *display_wayland = GDK_WAYLAND_DISPLAY (gdk_window_get_display (window));
@@ -638,7 +638,7 @@ window_update_scale (GdkWindow *window)
   for (c = children; c; c = c->next)
     {
       GdkWindow *child = c->data;
-      window_update_scale (child);
+      gdk_wayland_window_update_scale (child);
     }
   g_list_free (children);
 }
@@ -693,6 +693,9 @@ _gdk_wayland_display_create_window_impl (GdkDisplay    *display,
       break;
     }
 
+  if (real_parent == NULL)
+    display_wayland->toplevels = g_list_prepend (display_wayland->toplevels, window);
+
   gdk_wayland_window_create_surface (window);
 
   frame_clock = gdk_window_get_frame_clock (window);
@@ -1238,7 +1241,7 @@ surface_enter (void              *data,
 
   impl->display_server.outputs = g_slist_prepend (impl->display_server.outputs, output);
 
-  window_update_scale (window);
+  gdk_wayland_window_update_scale (window);
 }
 
 static void
@@ -1255,7 +1258,7 @@ surface_leave (void              *data,
   impl->display_server.outputs = g_slist_remove (impl->display_server.outputs, output);
 
   if (impl->display_server.outputs)
-    window_update_scale (window);
+    gdk_wayland_window_update_scale (window);
 }
 
 static const struct wl_surface_listener surface_listener = {
@@ -2835,6 +2838,12 @@ gdk_wayland_window_destroy (GdkWindow *window,
 
   gdk_wayland_window_hide_surface (window);
   drop_cairo_surfaces (window);
+
+  if (window->parent == NULL)
+    {
+      GdkWaylandDisplay *display = GDK_WAYLAND_DISPLAY (gdk_window_get_display (window));
+      display->toplevels = g_list_remove (display->toplevels, window);
+    }
 }
 
 static void