diff --git a/src/mswm/utils/checkpoint_restart.py b/src/mswm/utils/checkpoint_restart.py
index 8d26d8b0..943476f9 100644
--- a/src/mswm/utils/checkpoint_restart.py
+++ b/src/mswm/utils/checkpoint_restart.py
@@ -63,18 +63,14 @@ def checkpoint_restart(
         logger.critical(msg)
         raise FileNotFoundError(msg)
 
-    # Validate checkpoint state path exists
-    if not checkpoint_state.exists():
-        msg = f"Checkpoint state path does not exist: {checkpoint_state}"
-        logger.critical(msg)
-        raise FileNotFoundError(msg)
-
     # Fild realization file in the destination folder
     realization_files = list(dst.rglob("*realization*.json"))
     if not realization_files:
         msg = f"No realization file found in destination folder: {dst}"
         logger.critical(msg)
         raise FileNotFoundError(msg)
+    if len(realization_files) > 1:
+        logger.warning("More than one realization file found in source folder")
     realization_file = realization_files[0]
 
     # Read realization file
@@ -84,7 +80,16 @@ def checkpoint_restart(
     except json.JSONDecodeError as e:
         msg = f"Error parsing realization file: {realization_file}\n{e}"
         logger.critical(msg)
-        raise json.JSONDecodeError(msg) from e
+        raise ValueError(msg) from e
+
+    # Check that run used NetCDF catchment output writing
+    output_format = real_config.get("output_format", [])
+    if output_format == ["CSV"]:
+        msg = "output_format is set to ['CSV'] in realization file. Run cannot be restarted as catchment outputs will be incomplete."
+        logger.critical(msg)
+        raise ValueError(msg)
+    elif "NetCDF" in output_format and "CSV" in output_format:
+        logger.warning("output_format includes both 'NetCDF' and 'CSV' in realization file. CSV catchment outputs will be incomplete for restarted run.")
 
     # Build checkpoint state loading configuration
     load_config = {
diff --git a/tests/test_checkpoint.py b/tests/test_checkpoint.py
index 13b07754..a13655df 100644
--- a/tests/test_checkpoint.py
+++ b/tests/test_checkpoint.py
@@ -59,6 +59,14 @@ def checkpoint_run_folder(region_build, tmp_path):
     state.mkdir(exist_ok=True)
     (state / "cat-1_state").write_text("{}")
 
+    # Ensure output_format doesn't trigger CSV-only validation error
+    real_file = Path(region_build.realization_file)
+    with open(real_file) as f:
+        data = json.load(f)
+    data["output_format"] = ["NetCDF"]
+    with open(real_file, "w") as f:
+        json.dump(data, f)
+
     checkpoint_restart(str(src), str(dst))
     real_file = list(dst.rglob("*realization*.json"))[0]
     with open(real_file) as f:
@@ -189,3 +197,23 @@ def test_no_realization_file_raises(self, tmp_path):
                 str(empty_src),
                 str(tmp_path / "dst2")
             )
+
+    def test_csv_output_format_raises(self, region_build, tmp_path):
+        real_file = Path(region_build.realization_file)
+        with open(real_file) as f:
+            data = json.load(f)
+        data["output_format"] = ["CSV"]
+        with open(real_file, "w") as f:
+            json.dump(data, f)
+
+        src = Path(region_build.work_dir)
+        state = src / "checkpoint"
+        state.mkdir(exist_ok=True)
+        (state / "cat-1_state").write_text("{}")
+
+        dst = tmp_path / "dst_csv_only"
+
+        with pytest.raises(ValueError):
+            checkpoint_restart(
+                str(src), str(dst)
+            )