diff --git a/storage/local/persistence.go b/storage/local/persistence.go
index ef173f211..4d2733496 100644
--- a/storage/local/persistence.go
+++ b/storage/local/persistence.go
@@ -668,8 +668,10 @@ func (p *persistence) checkpointSeriesMapAndHeads(fingerprintToSeries *seriesMap
 			fpLocker.Lock(m.fp)
 			defer fpLocker.Unlock(m.fp)
 
-			if len(m.series.chunkDescs) == 0 {
-				// This series was completely purged or archived in the meantime. Ignore.
+			chunksToPersist := len(m.series.chunkDescs) - m.series.persistWatermark
+			if len(m.series.chunkDescs) == 0 || chunksToPersist == 0 {
+				// This series was completely purged or archived in the meantime or has
+				// no chunks that need persisting. Ignore.
 				return
 			}
 			realNumberOfSeries++
@@ -688,7 +690,9 @@ func (p *persistence) checkpointSeriesMapAndHeads(fingerprintToSeries *seriesMap
 			if _, err = w.Write(buf); err != nil {
 				return
 			}
-			if _, err = codable.EncodeVarint(w, int64(m.series.persistWatermark)); err != nil {
+			// persistWatermark. We only checkpoint chunks that need persisting, so
+			// this is always 0.
+			if _, err = codable.EncodeVarint(w, int64(0)); err != nil {
 				return
 			}
 			if m.series.modTime.IsZero() {
@@ -700,37 +704,25 @@ func (p *persistence) checkpointSeriesMapAndHeads(fingerprintToSeries *seriesMap
 					return
 				}
 			}
-			if _, err = codable.EncodeVarint(w, int64(m.series.chunkDescsOffset)); err != nil {
+			// chunkDescsOffset.
+			if _, err = codable.EncodeVarint(w, int64(m.series.chunkDescsOffset+m.series.persistWatermark)); err != nil {
 				return
 			}
 			if _, err = codable.EncodeVarint(w, int64(m.series.savedFirstTime)); err != nil {
 				return
 			}
-			if _, err = codable.EncodeVarint(w, int64(len(m.series.chunkDescs))); err != nil {
+			// Number of chunkDescs.
+			if _, err = codable.EncodeVarint(w, int64(chunksToPersist)); err != nil {
 				return
 			}
-			for i, chunkDesc := range m.series.chunkDescs {
-				if i < m.series.persistWatermark {
-					if _, err = codable.EncodeVarint(w, int64(chunkDesc.FirstTime())); err != nil {
-						return
-					}
-					lt, err := chunkDesc.LastTime()
-					if err != nil {
-						return
-					}
-					if _, err = codable.EncodeVarint(w, int64(lt)); err != nil {
-						return
-					}
-				} else {
-					// This is a non-persisted chunk. Fully marshal it.
-					if err = w.WriteByte(byte(chunkDesc.C.Encoding())); err != nil {
-						return
-					}
-					if err = chunkDesc.C.Marshal(w); err != nil {
-						return
-					}
+			for _, chunkDesc := range m.series.chunkDescs[m.series.persistWatermark:] {
+				if err = w.WriteByte(byte(chunkDesc.C.Encoding())); err != nil {
+					return
+				}
+				if err = chunkDesc.C.Marshal(w); err != nil {
+					return
 				}
-				p.checkpointChunksWritten.Observe(float64(len(m.series.chunkDescs) - m.series.persistWatermark))
+				p.checkpointChunksWritten.Observe(float64(chunksToPersist))
 			}
 			// Series is checkpointed now, so declare it clean. In case the entire
 			// checkpoint fails later on, this is fine, as the storage's series
diff --git a/storage/local/persistence_test.go b/storage/local/persistence_test.go
index 2b3785766..27f620366 100644
--- a/storage/local/persistence_test.go
+++ b/storage/local/persistence_test.go
@@ -493,8 +493,8 @@ func testCheckpointAndLoadSeriesMapAndHeads(t *testing.T, encoding chunk.Encodin
 	if err != nil {
 		t.Fatal(err)
 	}
-	if loadedSM.length() != 4 {
-		t.Errorf("want 4 series in map, got %d", loadedSM.length())
+	if loadedSM.length() != 3 {
+		t.Errorf("want 3 series in map, got %d", loadedSM.length())
 	}
 	if loadedS1, ok := loadedSM.get(m1.FastFingerprint()); ok {
 		if !reflect.DeepEqual(loadedS1.metric, m1) {
@@ -518,28 +518,6 @@ func testCheckpointAndLoadSeriesMapAndHeads(t *testing.T, encoding chunk.Encodin
 	} else {
 		t.Errorf("couldn't find %v in loaded map", m1)
 	}
-	if loadedS3, ok := loadedSM.get(m3.FastFingerprint()); ok {
-		if !reflect.DeepEqual(loadedS3.metric, m3) {
-			t.Errorf("want metric %v, got %v", m3, loadedS3.metric)
-		}
-		if loadedS3.head().C != nil {
-			t.Error("head chunk not evicted")
-		}
-		if loadedS3.chunkDescsOffset != 0 {
-			t.Errorf("want chunkDescsOffset 0, got %d", loadedS3.chunkDescsOffset)
-		}
-		if !loadedS3.headChunkClosed {
-			t.Error("headChunkClosed is false")
-		}
-		if loadedS3.head().ChunkFirstTime != 2 {
-			t.Errorf("want ChunkFirstTime in head chunk to be 2, got %d", loadedS3.head().ChunkFirstTime)
-		}
-		if loadedS3.head().ChunkLastTime != 2 {
-			t.Errorf("want ChunkLastTime in head chunk to be 2, got %d", loadedS3.head().ChunkLastTime)
-		}
-	} else {
-		t.Errorf("couldn't find %v in loaded map", m3)
-	}
 	if loadedS4, ok := loadedSM.get(m4.FastFingerprint()); ok {
 		if !reflect.DeepEqual(loadedS4.metric, m4) {
 			t.Errorf("want metric %v, got %v", m4, loadedS4.metric)
@@ -594,20 +572,17 @@ func testCheckpointAndLoadSeriesMapAndHeads(t *testing.T, encoding chunk.Encodin
 		if !reflect.DeepEqual(loadedS5.metric, m5) {
 			t.Errorf("want metric %v, got %v", m5, loadedS5.metric)
 		}
-		if got, want := len(loadedS5.chunkDescs), chunkCountS5; got != want {
+		if got, want := len(loadedS5.chunkDescs), chunkCountS5-3; got != want {
 			t.Errorf("got %d chunkDescs, want %d", got, want)
 		}
-		if got, want := loadedS5.persistWatermark, 3; got != want {
+		if got, want := loadedS5.persistWatermark, 0; got != want {
 			t.Errorf("got persistWatermark %d, want %d", got, want)
 		}
-		if !loadedS5.chunkDescs[2].IsEvicted() {
-			t.Error("3rd chunk not evicted")
-		}
-		if loadedS5.chunkDescs[3].IsEvicted() {
-			t.Error("4th chunk evicted")
+		if loadedS5.chunkDescs[0].IsEvicted() {
+			t.Error("1st chunk evicted")
 		}
-		if loadedS5.chunkDescsOffset != 0 {
-			t.Errorf("want chunkDescsOffset 0, got %d", loadedS5.chunkDescsOffset)
+		if loadedS5.chunkDescsOffset != 3 {
+			t.Errorf("want chunkDescsOffset 3, got %d", loadedS5.chunkDescsOffset)
 		}
 		if loadedS5.headChunkClosed {
 			t.Error("headChunkClosed is true")