Index: src/bp-activity/bp-activity-notifications.php
===================================================================
--- src/bp-activity/bp-activity-notifications.php
+++ src/bp-activity/bp-activity-notifications.php
@@ -55,7 +55,7 @@
 				$text   = sprintf( __( 'You have %1$d new replies', 'buddypress' ), (int) $total_items );
 				$amount = 'multiple';
 			} else {
-				$link = add_query_arg( 'nid', (int) $id, bp_activity_get_permalink( $activity_id ) );
+				$link = add_query_arg( 'rid', (int) $id, bp_activity_get_permalink( $activity_id ) );
 				$text = sprintf( __( '%1$s commented on one of your updates', 'buddypress' ), $user_fullname );
 			}
 		break;
@@ -70,8 +70,8 @@
 				$text   = sprintf( __( 'You have %1$d new comment replies', 'buddypress' ), (int) $total_items );
 				$amount = 'multiple';
 			} else {
-				$link = add_query_arg( 'nid', (int) $id, bp_activity_get_permalink( $activity_id ) );
-				$text = sprintf( __( '%1$s replied to one your activity comments', 'buddypress' ), $user_fullname );
+				$link = add_query_arg( 'crid', (int) $id, bp_activity_get_permalink( $activity_id ) );
+				$text = sprintf( __( '%1$s replied to one of your activity comments', 'buddypress' ), $user_fullname );
 			}
 		break;
 	}
@@ -239,6 +239,32 @@
 
 	// Mark as read any notifications for the current user related to this activity item.
 	bp_notifications_mark_notifications_by_item_id( bp_loggedin_user_id(), $activity->id, buddypress()->activity->id, 'new_at_mention' );
+
+	// For replies to a parent update.
+	if ( ! empty( $_GET['rid'] ) ) {
+		BP_Notifications_Notification::update(
+			array(
+				'is_new' => false
+			),
+			array(
+				'user_id' => bp_loggedin_user_id(),
+				'id'      => (int) $_GET['rid'],
+			)
+		);
+	}
+
+	// For replies to an activity comment.
+	if ( ! empty( $_GET['crid'] ) ) {
+		BP_Notifications_Notification::update(
+			array(
+				'is_new' => false
+			),
+			array(
+				'user_id' => bp_loggedin_user_id(),
+				'id'      => (int) $_GET['crid'],
+			)
+		);
+	}
 }
 add_action( 'bp_activity_screen_single_activity_permalink', 'bp_activity_remove_screen_notifications_single_activity_permalink' );