diff --git a/Source/Core/Core/WiiUtils.cpp b/Source/Core/Core/WiiUtils.cpp
index 30225febfbc3..92c2c19a0d98 100644
--- a/Source/Core/Core/WiiUtils.cpp
+++ b/Source/Core/Core/WiiUtils.cpp
@@ -961,6 +961,34 @@ static NANDCheckResult CheckNAND(IOS::HLE::Kernel& ios, bool repair)
     }
   }
 
+  // Get some storage stats.
+  const auto fs = ios.GetFS();
+  const auto root_stats = fs->GetExtendedDirectoryStats("/");
+
+  // The Wii System Menu's save/channel management only considers a specific subset of the Wii NAND
+  // user-accessible and will only use those folders when calculating the amount of free blocks it
+  // displays. This can have weird side-effects where the other parts of the NAND contain more data
+  // than reserved and it will display free blocks even though there isn't any space left. To avoid
+  // confusion, report the 'user' and 'system' data separately to the user.
+  u64 used_clusters_user = 0;
+  u64 used_inodes_user = 0;
+  for (std::string user_path : {"/meta", "/ticket", "/title/00010000", "/title/00010001",
+                                "/title/00010003", "/title/00010004", "/title/00010005",
+                                "/title/00010006", "/title/00010007", "/shared2/title"})
+  {
+    const auto dir_stats = fs->GetExtendedDirectoryStats(user_path);
+    if (dir_stats)
+    {
+      used_clusters_user += dir_stats->used_clusters;
+      used_inodes_user += dir_stats->used_inodes;
+    }
+  }
+
+  result.used_clusters_user = used_clusters_user;
+  result.used_clusters_system = root_stats ? (root_stats->used_clusters - used_clusters_user) : 0;
+  result.used_inodes_user = used_inodes_user;
+  result.used_inodes_system = root_stats ? (root_stats->used_inodes - used_inodes_user) : 0;
+
   return result;
 }
 
diff --git a/Source/Core/Core/WiiUtils.h b/Source/Core/Core/WiiUtils.h
index ae2d7c85e080..c8f86d7253c0 100644
--- a/Source/Core/Core/WiiUtils.h
+++ b/Source/Core/Core/WiiUtils.h
@@ -101,6 +101,10 @@ struct NANDCheckResult
 {
   bool bad = false;
   std::unordered_set<u64> titles_to_remove;
+  u64 used_clusters_user = 0;
+  u64 used_clusters_system = 0;
+  u64 used_inodes_user = 0;
+  u64 used_inodes_system = 0;
 };
 NANDCheckResult CheckNAND(IOS::HLE::Kernel& ios);
 bool RepairNAND(IOS::HLE::Kernel& ios);
diff --git a/Source/Core/DolphinQt/MenuBar.cpp b/Source/Core/DolphinQt/MenuBar.cpp
index b0989fae66af..f1c6ea2993f9 100644
--- a/Source/Core/DolphinQt/MenuBar.cpp
+++ b/Source/Core/DolphinQt/MenuBar.cpp
@@ -15,6 +15,7 @@
 #include <QMap>
 #include <QUrl>
 
+#include "Common/Align.h"
 #include "Common/CommonPaths.h"
 #include "Common/FileUtil.h"
 #include "Common/StringUtil.h"
@@ -32,6 +33,7 @@
 #include "Core/HW/WiiSave.h"
 #include "Core/HW/Wiimote.h"
 #include "Core/IOS/ES/ES.h"
+#include "Core/IOS/FS/FileSystem.h"
 #include "Core/IOS/IOS.h"
 #include "Core/IOS/USB/Bluetooth/BTEmu.h"
 #include "Core/Movie.h"
@@ -1137,7 +1139,42 @@ void MenuBar::CheckNAND()
   WiiUtils::NANDCheckResult result = WiiUtils::CheckNAND(ios);
   if (!result.bad)
   {
-    ModalMessageBox::information(this, tr("NAND Check"), tr("No issues have been detected."));
+    const bool overfull = result.used_clusters_user > IOS::HLE::FS::USER_CLUSTERS ||
+                          result.used_clusters_system > IOS::HLE::FS::SYSTEM_CLUSTERS;
+    const QString user_cluster_message =
+        tr("The user-accessible part of your NAND contains %1 blocks (%2 KiB) "
+           "of data, out of an allowed maximum of %3 blocks (%4 KiB).")
+            .arg(Common::AlignUp(result.used_clusters_user, IOS::HLE::FS::CLUSTERS_PER_BLOCK) /
+                 IOS::HLE::FS::CLUSTERS_PER_BLOCK)
+            .arg((result.used_clusters_user * IOS::HLE::FS::CLUSTER_SIZE) / 1024)
+            .arg(IOS::HLE::FS::USER_CLUSTERS / IOS::HLE::FS::CLUSTERS_PER_BLOCK)
+            .arg((IOS::HLE::FS::USER_CLUSTERS * IOS::HLE::FS::CLUSTER_SIZE) / 1024);
+    const QString system_cluster_message =
+        tr("The system-reserved part of your NAND contains %1 blocks (%2 KiB) "
+           "of data, out of an allowed maximum of %3 blocks (%4 KiB).")
+            .arg(Common::AlignUp(result.used_clusters_system, IOS::HLE::FS::CLUSTERS_PER_BLOCK) /
+                 IOS::HLE::FS::CLUSTERS_PER_BLOCK)
+            .arg((result.used_clusters_system * IOS::HLE::FS::CLUSTER_SIZE) / 1024)
+            .arg(IOS::HLE::FS::SYSTEM_CLUSTERS / IOS::HLE::FS::CLUSTERS_PER_BLOCK)
+            .arg((IOS::HLE::FS::SYSTEM_CLUSTERS * IOS::HLE::FS::CLUSTER_SIZE) / 1024);
+
+    if (overfull)
+    {
+      ModalMessageBox::warning(this, tr("NAND Check"),
+                               QStringLiteral("%1\n\n%2\n\n%3")
+                                   .arg(tr("Your NAND contains more data than allowed. Wii "
+                                           "software may behave incorrectly or not allow saving."))
+                                   .arg(user_cluster_message)
+                                   .arg(system_cluster_message));
+    }
+    else
+    {
+      ModalMessageBox::information(this, tr("NAND Check"),
+                                   QStringLiteral("%1\n\n%2\n\n%3")
+                                       .arg(tr("No issues have been detected."))
+                                       .arg(user_cluster_message)
+                                       .arg(system_cluster_message));
+    }
     return;
   }