diff --git a/src/saveload/waypoint_sl.cpp b/src/saveload/waypoint_sl.cpp
--- a/src/saveload/waypoint_sl.cpp
+++ b/src/saveload/waypoint_sl.cpp
@@ -5,120 +5,187 @@
 #include "../stdafx.h"
 #include "../waypoint.h"
 #include "../newgrf_station.h"
+#include "../vehicle_base.h"
 #include "../town.h"
+#include "../station_map.h"
 
 #include "table/strings.h"
 
 #include "saveload.h"
 #include "saveload_internal.h"
 
-/**
- * Update waypoint graphics id against saved GRFID/localidx.
- * This is to ensure the chosen graphics are correct if GRF files are changed.
- */
-void AfterLoadWaypoints()
-{
-	Waypoint *wp;
+/** Helper structure to convert from the old waypoint system. */
+struct OldWaypoint {
+	size_t index;
+	TileIndex xy;
+	TownID town_index;
+	Town *town;
+	uint16 town_cn;
+	StringID string_id;
+	char *name;
+	uint8 delete_ctr;
+	Date build_date;
+	uint8 localidx;
+	uint32 grfid;
+	const StationSpec *spec;
+	OwnerByte owner;
 
-	FOR_ALL_WAYPOINTS(wp) {
-		if (wp->num_specs == 0) continue;
+	size_t new_index;
+};
+
+/** Temporary array with old waypoints. */
+static SmallVector<OldWaypoint, 16> _old_waypoints;
 
-		for (uint i = 0; i < GetNumCustomStations(STAT_CLASS_WAYP); i++) {
-			const StationSpec *statspec = GetCustomStationSpec(STAT_CLASS_WAYP, i);
-			if (statspec != NULL && statspec->grffile->grfid == wp->speclist[1].grfid && statspec->localidx == wp->speclist[1].localidx) {
-				wp->speclist[1].spec = statspec;
-				break;
-			}
-		}
+/**
+ * Update the waypoint orders to get the new waypoint ID.
+ * @param o the order 'list' to check.
+ */
+static void UpdateWaypointOrder(Order *o)
+{
+	if (!o->IsType(OT_GOTO_WAYPOINT)) return;
+
+	for (OldWaypoint *wp = _old_waypoints.Begin(); wp != _old_waypoints.End(); wp++) {
+		if (wp->index != o->GetDestination()) continue;
+
+		o->SetDestination(wp->new_index);
+		return;
 	}
 }
 
-static uint16 _waypoint_town_index;
-static StringID _waypoint_string_id;
-static StationSpecList _waypoint_spec;
+/**
+ * Perform all steps to upgrade from the old waypoints to the new version
+ * that uses station. This includes some old saveload mechanics.
+ */
+void MoveWaypointsToBaseStations()
+{
+	/* In version 17, ground type is moved from m2 to m4 for depots and
+	 * waypoints to make way for storing the index in m2. The custom graphics
+	 * id which was stored in m4 is now saved as a grf/id reference in the
+	 * waypoint struct. */
+	if (CheckSavegameVersion(17)) {
+		for (OldWaypoint *wp = _old_waypoints.Begin(); wp != _old_waypoints.End(); wp++) {
+			if (wp->delete_ctr == 0 && HasBit(_m[wp->xy].m3, 4)) {
+				wp->spec = GetCustomStationSpec(STAT_CLASS_WAYP, _m[wp->xy].m4 + 1);
+			}
+		}
+	} else {
+		/* As of version 17, we recalculate the custom graphic ID of waypoints
+		 * from the GRF ID / station index. */
+		for (OldWaypoint *wp = _old_waypoints.Begin(); wp != _old_waypoints.End(); wp++) {
+			for (uint i = 0; i < GetNumCustomStations(STAT_CLASS_WAYP); i++) {
+				const StationSpec *statspec = GetCustomStationSpec(STAT_CLASS_WAYP, i);
+				if (statspec != NULL && statspec->grffile->grfid == wp->grfid && statspec->localidx == wp->localidx) {
+					wp->spec = statspec;
+					break;
+				}
+			}
+		}
+	}
+
+	/* All saveload conversions have been done. Create the new waypoints! */
+	for (OldWaypoint *wp = _old_waypoints.Begin(); wp != _old_waypoints.End(); wp++) {
+		Waypoint *new_wp = new Waypoint(wp->xy);
+		new_wp->town       = wp->town;
+		new_wp->town_cn    = wp->town_cn;
+		new_wp->name       = wp->name;
+		new_wp->delete_ctr = 0; // Just reset delete counter for once.
+		new_wp->build_date = wp->build_date;
+		new_wp->owner      = wp->owner;
+
+		new_wp->string_id = STR_SV_STNAME_WAYPOINT;
+
+		TileIndex t = wp->xy;
+		if (IsTileType(t, MP_RAILWAY) && GetRailTileType(t) == 2 /* RAIL_TILE_WAYPOINT */ && _m[t].m2 == wp->index) {
+			/* The tile might've been reserved! */
+			bool reserved = !CheckSavegameVersion(100) && HasBit(_m[t].m5, 4);
 
-static const SaveLoad _waypoint_desc[] = {
-	 SLE_CONDVAR(Waypoint, xy,            SLE_FILE_U16 | SLE_VAR_U32,  0, 5),
-	 SLE_CONDVAR(Waypoint, xy,            SLE_UINT32,                  6, SL_MAX_VERSION),
-	SLEG_CONDVAR(_waypoint_town_index,    SLE_UINT16,                 12, 121),
-	 SLE_CONDREF(Waypoint, town,          REF_TOWN,                  122, SL_MAX_VERSION),
-	 SLE_CONDVAR(Waypoint, town_cn,       SLE_FILE_U8 | SLE_VAR_U16,  12, 88),
-	 SLE_CONDVAR(Waypoint, town_cn,       SLE_UINT16,                 89, SL_MAX_VERSION),
-	SLEG_CONDVAR(_waypoint_string_id,     SLE_STRINGID,                0, 83),
-	 SLE_CONDSTR(Waypoint, name,          SLE_STR, 0,                 84, SL_MAX_VERSION),
-	     SLE_VAR(Waypoint, delete_ctr,    SLE_UINT8),
+			/* The tile really has our waypoint, so reassign the map array */
+			MakeRailWaypoint(t, GetTileOwner(t), new_wp->index, (Axis)GB(_m[t].m5, 0, 1), 0, GetRailType(t));
+			new_wp->facilities |= FACIL_TRAIN;
+			new_wp->owner = GetTileOwner(t);
+
+			SetRailwayStationReservation(t, reserved);
+
+			if (wp->spec != NULL) {
+				SetCustomStationSpecIndex(t, AllocateSpecToStation(wp->spec, new_wp, true));
+			}
+		}
+
+		wp->new_index = new_wp->index;
+	}
+
+	/* Update the orders of vehicles */
+	OrderList *ol;
+	FOR_ALL_ORDER_LISTS(ol) {
+		if (ol->GetFirstSharedVehicle()->type != VEH_TRAIN) continue;
+
+		for (Order *o = ol->GetFirstOrder(); o != NULL; o = o->next) UpdateWaypointOrder(o);
+	}
 
-	 SLE_CONDVAR(Waypoint, build_date,    SLE_FILE_U16 | SLE_VAR_I32,  3, 30),
-	 SLE_CONDVAR(Waypoint, build_date,    SLE_INT32,                  31, SL_MAX_VERSION),
-	SLEG_CONDVAR(_waypoint_spec.localidx, SLE_UINT8,                   3, SL_MAX_VERSION),
-	SLEG_CONDVAR(_waypoint_spec.grfid,    SLE_UINT32,                 17, SL_MAX_VERSION),
-	 SLE_CONDVAR(Waypoint, owner,         SLE_UINT8,                 101, SL_MAX_VERSION),
+	Vehicle *v;
+	FOR_ALL_VEHICLES(v) {
+		if (v->type != VEH_TRAIN) continue;
+
+		UpdateWaypointOrder(&v->current_order);
+	}
+
+	_old_waypoints.Reset();
+}
+
+static const SaveLoad _old_waypoint_desc[] = {
+	SLE_CONDVAR(OldWaypoint, xy,         SLE_FILE_U16 | SLE_VAR_U32,  0, 5),
+	SLE_CONDVAR(OldWaypoint, xy,         SLE_UINT32,                  6, SL_MAX_VERSION),
+	SLE_CONDVAR(OldWaypoint, town_index, SLE_UINT16,                 12, 121),
+	SLE_CONDREF(OldWaypoint, town,       REF_TOWN,                  122, SL_MAX_VERSION),
+	SLE_CONDVAR(OldWaypoint, town_cn,    SLE_FILE_U8 | SLE_VAR_U16,  12, 88),
+	SLE_CONDVAR(OldWaypoint, town_cn,    SLE_UINT16,                 89, SL_MAX_VERSION),
+	SLE_CONDVAR(OldWaypoint, string_id,  SLE_STRINGID,                0, 83),
+	SLE_CONDSTR(OldWaypoint, name,       SLE_STR, 0,                 84, SL_MAX_VERSION),
+	    SLE_VAR(OldWaypoint, delete_ctr, SLE_UINT8),
+
+	SLE_CONDVAR(OldWaypoint, build_date, SLE_FILE_U16 | SLE_VAR_I32,  3, 30),
+	SLE_CONDVAR(OldWaypoint, build_date, SLE_INT32,                  31, SL_MAX_VERSION),
+	SLE_CONDVAR(OldWaypoint, localidx,   SLE_UINT8,                   3, SL_MAX_VERSION),
+	SLE_CONDVAR(OldWaypoint, grfid,      SLE_UINT32,                 17, SL_MAX_VERSION),
+	SLE_CONDVAR(OldWaypoint, owner,      SLE_UINT8,                 101, SL_MAX_VERSION),
 
 	SLE_END()
 };
 
-static void Save_WAYP()
-{
-	Waypoint *wp;
-
-	FOR_ALL_WAYPOINTS(wp) {
-		if (wp->num_specs == 0) {
-			_waypoint_spec.grfid = 0;
-		} else {
-			_waypoint_spec = wp->speclist[1];
-		}
-
-		SlSetArrayIndex(wp->index);
-		SlObject(wp, _waypoint_desc);
-	}
-}
-
 static void Load_WAYP()
 {
+	/* Precaution for when loading failed and it didn't get cleared */
+	_old_waypoints.Clear();
+
 	int index;
 
 	while ((index = SlIterateArray()) != -1) {
-		_waypoint_string_id = 0;
-		_waypoint_town_index = 0;
-		_waypoint_spec.grfid = 0;
-
-		Waypoint *wp = new (index) Waypoint();
-		SlObject(wp, _waypoint_desc);
-
-		wp->facilities |= FACIL_TRAIN;
+		OldWaypoint *wp = _old_waypoints.Append();
+		memset(wp, 0, sizeof(*wp));
 
-		if (_waypoint_spec.grfid != 0) {
-			wp->num_specs = 2;
-			wp->speclist = CallocT<StationSpecList>(2);
-			wp->speclist[1] = _waypoint_spec;
-		}
-
-		if (CheckSavegameVersion(84)) wp->name = (char *)(size_t)_waypoint_string_id;
-		if (CheckSavegameVersion(122)) wp->town = (Town *)(size_t)_waypoint_town_index;
+		wp->index = index;
+		SlObject(wp, _old_waypoint_desc);
 	}
 }
 
 static void Ptrs_WAYP()
 {
-	Waypoint *wp;
+	for (OldWaypoint *wp = _old_waypoints.Begin(); wp != _old_waypoints.End(); wp++) {
+		SlObject(wp, _old_waypoint_desc);
 
-	FOR_ALL_WAYPOINTS(wp) {
-		SlObject(wp, _waypoint_desc);
-
-		StringID sid = (StringID)(size_t)wp->name;
 		if (CheckSavegameVersion(12)) {
-			wp->town_cn = (sid & 0xC000) == 0xC000 ? (sid >> 8) & 0x3F : 0;
+			wp->town_cn = (wp->string_id & 0xC000) == 0xC000 ? (wp->string_id >> 8) & 0x3F : 0;
 			wp->town = ClosestTownFromTile(wp->xy, UINT_MAX);
 		} else if (CheckSavegameVersion(122)) {
 			/* Only for versions 12 .. 122 */
-			wp->town = Town::Get((size_t)wp->town);
+			wp->town = Town::Get(wp->town_index);
 		}
 		if (CheckSavegameVersion(84)) {
-			wp->name = CopyFromOldName(sid);
+			wp->name = CopyFromOldName(wp->string_id);
 		}
 	}
 }
 
 extern const ChunkHandler _waypoint_chunk_handlers[] = {
-	{ 'CHKP', Save_WAYP, Load_WAYP, Ptrs_WAYP, CH_ARRAY | CH_LAST},
+	{ 'CHKP', NULL, Load_WAYP, Ptrs_WAYP, CH_ARRAY | CH_LAST},
 };