diff -u b/core/modules/migrate/src/Plugin/migrate/source/SqlBase.php b/core/modules/migrate/src/Plugin/migrate/source/SqlBase.php
--- b/core/modules/migrate/src/Plugin/migrate/source/SqlBase.php
+++ b/core/modules/migrate/src/Plugin/migrate/source/SqlBase.php
@@ -128,6 +128,7 @@
       }
     }
     else {
+      /** @var \Drupal\Core\Database\Query\Condition $conditions */
       $conditions = $this->query->orConditionGroup();
       // 1. If the map is joinable, join it. We will want to accept all rows
       //    which are either not in the map, or marked in the map as NEEDS_UPDATE.
@@ -137,10 +138,12 @@
       //    conditions in the query). So, ultimately the SQL condition will look
       //    like (original conditions) AND (map IS NULL OR map needs update
       //    OR above high water).
-      //
+      $this->joinMapTable($conditions);
       // 2. If we are using high water marks, also include rows above the mark.
       //    But, include all rows if the high water mark is not set.
-      if ($this->joinMapTable($conditions) || $this->addHighWaterProperty($conditions)) {
+      $this->addHighWaterProperty($conditions);
+
+      if ($conditions->count() > 0) {
         $this->query->condition($conditions);
       }
     }