diff --git a/core/src/graph.jl b/core/src/graph.jl
index 666591e8e..e2a3273e0 100644
--- a/core/src/graph.jl
+++ b/core/src/graph.jl
@@ -19,8 +19,7 @@ function create_graph(db::DB, config::Config)::MetaGraph
             FromNode.node_type AS from_node_type,
             ToNode.node_id AS to_node_id,
             ToNode.node_type AS to_node_type,
-            Edge.edge_type,
-            Edge.subnetwork_id
+            Edge.edge_type
         FROM Edge
         LEFT JOIN Node AS FromNode ON FromNode.node_id = Edge.from_node_id
         LEFT JOIN Node AS ToNode ON ToNode.node_id = Edge.to_node_id
diff --git a/core/src/model.jl b/core/src/model.jl
index e0047ca0d..2197d72b7 100644
--- a/core/src/model.jl
+++ b/core/src/model.jl
@@ -47,6 +47,7 @@ function Model(config::Config)::Model
     # so we can directly close it again.
     db = SQLite.DB(db_path)
 
+    database_warning(db)
     if !valid_nodes(db)
         error("Invalid nodes found.")
     end
diff --git a/core/src/validation.jl b/core/src/validation.jl
index 3eba4339a..81a372421 100644
--- a/core/src/validation.jl
+++ b/core/src/validation.jl
@@ -182,6 +182,14 @@ function valid_nodes(db::DB)::Bool
     return !errors
 end
 
+function database_warning(db::DB)::Nothing
+    cols = SQLite.columns(db, "Edge")
+    if "subnetwork_id" in cols.name
+        @warn "The 'subnetwork_id' column in the 'Edge' table is deprecated since ribasim v2024.12."
+    end
+    return nothing
+end
+
 """
 Test for each node given its node type whether the nodes that
 # are downstream ('down-edge') of this node are of an allowed type
diff --git a/docs/changelog.qmd b/docs/changelog.qmd
index d9c04350e..373ab6cc8 100644
--- a/docs/changelog.qmd
+++ b/docs/changelog.qmd
@@ -5,6 +5,9 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 
 ## [Unreleased]
 
+### Changed
+- The Edge table no longer supports `subnetwork_id`; this is automatically inferred. [#1956](https://github.com/Deltares/Ribasim/pull/1956)
+
 ## [v2024.11.0] - 2024-10-08
 
 This major new release contains many improvements.
diff --git a/python/ribasim/ribasim/geometry/edge.py b/python/ribasim/ribasim/geometry/edge.py
index 62a73cb28..faa2e92fa 100644
--- a/python/ribasim/ribasim/geometry/edge.py
+++ b/python/ribasim/ribasim/geometry/edge.py
@@ -47,7 +47,6 @@ class EdgeSchema(_GeoBaseSchema):
     from_node_id: Series[Int32] = pa.Field(default=0)
     to_node_id: Series[Int32] = pa.Field(default=0)
     edge_type: Series[str] = pa.Field(default="flow")
-    subnetwork_id: Series[pd.Int32Dtype] = pa.Field(default=pd.NA, nullable=True)
     geometry: GeoSeries[LineString] = pa.Field(default=None, nullable=True)
 
     @classmethod
@@ -73,7 +72,6 @@ def add(
         to_node: NodeData,
         geometry: LineString | MultiLineString | None = None,
         name: str = "",
-        subnetwork_id: int | None = None,
         edge_id: Optional[NonNegativeInt] = None,
         **kwargs,
     ):
@@ -90,6 +88,8 @@ def add(
             The geometry of a line. If not supplied, it creates a straight line between the nodes.
         name : str
             An optional name for the edge.
+        id : int
+            An optional non-negative edge ID. If not supplied, it will be automatically generated.
         **kwargs : Dict
         """
         if not can_connect(from_node.node_type, to_node.node_type):
@@ -120,7 +120,6 @@ def add(
                 "to_node_id": [to_node.node_id],
                 "edge_type": [edge_type],
                 "name": [name],
-                "subnetwork_id": [subnetwork_id],
                 **kwargs,
             },
             geometry=geometry_to_append,
diff --git a/python/ribasim/ribasim/migrations.py b/python/ribasim/ribasim/migrations.py
index 5f3e09d3c..31a326e83 100644
--- a/python/ribasim/ribasim/migrations.py
+++ b/python/ribasim/ribasim/migrations.py
@@ -27,7 +27,7 @@ def edgeschema_migration(gdf: GeoDataFrame, schema_version: int) -> GeoDataFrame
         warnings.warn("Migrating outdated Edge table.", UserWarning)
         assert gdf["edge_id"].is_unique, "Edge IDs have to be unique."
         gdf.set_index("edge_id", inplace=True)
-    if "subnetwork_id" in gdf.columns and schema_version == 0:
+    if "subnetwork_id" in gdf.columns:
         warnings.warn("Migrating outdated Edge table.", UserWarning)
         gdf.drop(columns="subnetwork_id", inplace=True, errors="ignore")
 
diff --git a/python/ribasim/tests/test_model.py b/python/ribasim/tests/test_model.py
index ba703d5fa..f5e341561 100644
--- a/python/ribasim/tests/test_model.py
+++ b/python/ribasim/tests/test_model.py
@@ -145,7 +145,6 @@ def test_edge_table(basic):
     df = model.edge.df
     assert df.geometry.is_unique
     assert df.from_node_id.dtype == np.int32
-    assert df.subnetwork_id.dtype == pd.Int32Dtype()
     assert df.crs == CRS.from_epsg(28992)
 
 
diff --git a/ribasim_qgis/core/nodes.py b/ribasim_qgis/core/nodes.py
index 9a1859c77..c638a58e0 100644
--- a/ribasim_qgis/core/nodes.py
+++ b/ribasim_qgis/core/nodes.py
@@ -253,7 +253,6 @@ def attributes(cls) -> list[QgsField]:
             QgsField("from_node_id", QVariant.Int),
             QgsField("to_node_id", QVariant.Int),
             QgsField("edge_type", QVariant.String),
-            QgsField("subnetwork_id", QVariant.Int),
         ]
 
     @classmethod