diff --git a/hydromt_sfincs/workflows/merge.py b/hydromt_sfincs/workflows/merge.py
index 0a90a252..8a21c86b 100644
--- a/hydromt_sfincs/workflows/merge.py
+++ b/hydromt_sfincs/workflows/merge.py
@@ -99,6 +99,7 @@ def merge_multi_dataarrays(
             # no data in da1 so use an empty array like da_like
             logger.debug("No data da1, start with empty array")
             da1 = xr.full_like(da_like, np.nan)
+            da1.raster.set_nodata(np.nan)
         else:
             # TODO: this applies to the whole dataset, not only the clipped part
             da1 = da1.load().raster.reproject_like(da_like)