diff --git a/crates/sui-indexer-alt/src/lib.rs b/crates/sui-indexer-alt/src/lib.rs
index fce20707677b5..08a7ec2b01554 100644
--- a/crates/sui-indexer-alt/src/lib.rs
+++ b/crates/sui-indexer-alt/src/lib.rs
@@ -3,7 +3,7 @@
 
 use std::{collections::BTreeSet, net::SocketAddr, sync::Arc};
 
-use anyhow::{Context, Result};
+use anyhow::{ensure, Context, Result};
 use db::{Db, DbConfig};
 use ingestion::{IngestionConfig, IngestionService};
 use metrics::{IndexerMetrics, MetricsService};
@@ -146,6 +146,13 @@ impl Indexer {
             return Ok(());
         };
 
+        // For a concurrent pipeline, if skip_watermark is set, we don't really care about the
+        // watermark consistency. first_checkpoint can be anything since we don't update watermark,
+        // and writes should be idempotent.
+        if !self.pipeline_config.skip_watermark {
+            self.check_first_checkpoint_consistency::<H>(&watermark)?;
+        }
+
         let (processor, collector, committer, watermark) = concurrent::pipeline::<H>(
             watermark,
             self.pipeline_config.clone(),
@@ -176,6 +183,10 @@ impl Indexer {
             return Ok(());
         };
 
+        // For a sequential pipeline, data must be written in the order of checkpoints.
+        // Hence, we do not allow the first_checkpoint override to be in arbitrary positions.
+        self.check_first_checkpoint_consistency::<H>(&watermark)?;
+
         let (checkpoint_rx, watermark_tx) = self.ingestion_service.subscribe();
 
         let (processor, committer) = sequential::pipeline::<H>(
@@ -194,6 +205,27 @@ impl Indexer {
         Ok(())
     }
 
+    /// Checks that the first checkpoint override is consistent with the watermark for the pipeline.
+    /// If the watermark does not exist, the override can be anything. If the watermark exists, the
+    /// override must not leave any gap in the data: it can be in the past, or at the tip of the
+    /// network, but not in the future.
+    fn check_first_checkpoint_consistency<P: Processor>(
+        &self,
+        watermark: &Option<CommitterWatermark>,
+    ) -> Result<()> {
+        if let (Some(watermark), Some(first_checkpoint)) = (watermark, self.first_checkpoint) {
+            ensure!(
+                first_checkpoint as i64 <= watermark.checkpoint_hi_inclusive + 1,
+                "For pipeline {}, first checkpoint override {} is too far ahead of watermark {}. This could create gaps in the data.",
+                P::NAME,
+                first_checkpoint,
+                watermark.checkpoint_hi_inclusive,
+            );
+        }
+
+        Ok(())
+    }
+
     /// Start ingesting checkpoints. Ingestion either starts from the configured
     /// `first_checkpoint`, or it is calculated based on the watermarks of all active pipelines.
     /// Ingestion will stop after consuming the configured `last_checkpoint`, if one is provided,
diff --git a/crates/sui-indexer-alt/src/pipeline/concurrent/watermark.rs b/crates/sui-indexer-alt/src/pipeline/concurrent/watermark.rs
index 481a581b06ec7..69b58e266f69c 100644
--- a/crates/sui-indexer-alt/src/pipeline/concurrent/watermark.rs
+++ b/crates/sui-indexer-alt/src/pipeline/concurrent/watermark.rs
@@ -179,6 +179,8 @@ pub(super) fn watermark<H: Handler + 'static>(
                             .with_label_values(&[H::NAME])
                             .start_timer();
 
+                        // TODO: If initial_watermark is empty, when we update watermark
+                        // for the first time, we should also update the low watermark.
                         match watermark.update(&mut conn).await {
                             // If there's an issue updating the watermark, log it but keep going,
                             // it's OK for the watermark to lag from a correctness perspective.
diff --git a/crates/sui-indexer-alt/src/pipeline/mod.rs b/crates/sui-indexer-alt/src/pipeline/mod.rs
index 576e308c61b0f..05949d524832a 100644
--- a/crates/sui-indexer-alt/src/pipeline/mod.rs
+++ b/crates/sui-indexer-alt/src/pipeline/mod.rs
@@ -54,7 +54,7 @@ pub struct PipelineConfig {
 
     /// Avoid writing to the watermark table
     #[arg(long)]
-    skip_watermark: bool,
+    pub skip_watermark: bool,
 }
 
 /// Processed values associated with a single checkpoint. This is an internal type used to
diff --git a/crates/sui-indexer-alt/src/pipeline/sequential/committer.rs b/crates/sui-indexer-alt/src/pipeline/sequential/committer.rs
index 3bd06518c9c10..663383fc8d1d9 100644
--- a/crates/sui-indexer-alt/src/pipeline/sequential/committer.rs
+++ b/crates/sui-indexer-alt/src/pipeline/sequential/committer.rs
@@ -182,6 +182,8 @@ pub(super) fn committer<H: Handler + 'static>(
                     // single transaction. The handler's `commit` implementation is responsible for
                     // chunking up the writes into a manageable size.
                     let affected = conn.transaction::<_, anyhow::Error, _>(|conn| async {
+                        // TODO: If initial_watermark is empty, when we update watermark
+                        // for the first time, we should also update the low watermark.
                         watermark.update(conn).await?;
                         H::commit(&batch, conn).await
                     }.scope_boxed()).await;