diff --git a/src/glide/cli.py b/src/glide/cli.py
index 4045581..f05baf9 100644
--- a/src/glide/cli.py
+++ b/src/glide/cli.py
@@ -210,13 +210,13 @@ def l3(
     """
     Generate L3 data from L2 data.
     """
+    conf = config.load_config(config_file)
+
     l2 = process_l2.parse_l2(l2_file)
 
-    out = process_l2.bin_l2(l2, bin_size, depth)
+    out = process_l2.bin_l2(l2, bin_size, depth, conf)
 
     if q_netcdf is not None:
-        conf = config.load_config(config_file)
-
         q = ancillery.parse_q(q_netcdf)
 
         out = process_l3.bin_q(out, q, bin_size, conf)
diff --git a/src/glide/process_l2.py b/src/glide/process_l2.py
index ddd1acb..0b9127d 100644
--- a/src/glide/process_l2.py
+++ b/src/glide/process_l2.py
@@ -59,7 +59,10 @@ def parse_l2(file: str) -> xr.Dataset:
 
 
 def bin_l2(
-    ds: xr.Dataset, bin_size: float = 10.0, depth: float | None = None
+    ds: xr.Dataset,
+    bin_size: float = 10.0,
+    depth: float | None = None,
+    config: dict | None = None,
 ) -> xr.Dataset:
     """Depth bin size specified in meters."""
 
@@ -80,6 +83,16 @@ def bin_l2(
     # treat them after binning. We may want to define new QC variables in the future.
     qc_variables = [v for v in ds.variables if "_qc" in str(v)]
     drop_variables = qc_variables + ["dive_id", "climb_id", "state", "z"]
+
+    # Drop variables flagged with drop_from_l3 in the config
+    if config is not None:
+        for v in list(ds.variables):
+            try:
+                if config["variables"][v].get("drop_from_l3", False):
+                    _log.info("Not binning %s due to drop_from_l3 flag in config", v)
+                    drop_variables.append(v)
+            except KeyError:
+                pass
     _log.warning("Binning QC flags is not supported, dropping %s", drop_variables)
     for var in ds.variables:
         if "ancillary_variables" not in ds[var].attrs: