diff --git a/Cargo.lock b/Cargo.lock
index 8eb2229c9a1dc..d40d2c4713dc6 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -361,8 +361,8 @@ dependencies = [
  "futures",
  "once_cell",
  "paste",
- "prost",
- "prost-types",
+ "prost 0.14.1",
+ "prost-types 0.14.1",
  "tonic",
  "tonic-prost",
 ]
@@ -1131,8 +1131,8 @@ version = "0.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "85a885520bf6249ab931a764ffdb87b0ceef48e6e7d807cfdb21b751e086e1ad"
 dependencies = [
- "prost",
- "prost-types",
+ "prost 0.14.1",
+ "prost-types 0.14.1",
  "tonic",
  "tonic-prost",
  "ureq",
@@ -1148,7 +1148,7 @@ dependencies = [
  "bollard-buildkit-proto",
  "bytes",
  "chrono",
- "prost",
+ "prost 0.14.1",
  "serde",
  "serde_json",
  "serde_repr",
@@ -2127,7 +2127,7 @@ dependencies = [
  "mimalloc",
  "nix",
  "object_store",
- "prost",
+ "prost 0.14.1",
  "rand 0.9.2",
  "serde_json",
  "strum 0.27.2",
@@ -2227,7 +2227,7 @@ dependencies = [
  "doc-comment",
  "futures",
  "log",
- "prost",
+ "prost 0.13.5",
  "semver",
  "tokio",
 ]
@@ -2536,9 +2536,9 @@ dependencies = [
  "datafusion-proto-common",
  "doc-comment",
  "object_store",
- "pbjson",
+ "pbjson 0.8.0",
  "pretty_assertions",
- "prost",
+ "prost 0.13.5",
  "serde",
  "serde_json",
  "tokio",
@@ -2551,8 +2551,8 @@ dependencies = [
  "arrow",
  "datafusion-common",
  "doc-comment",
- "pbjson",
- "prost",
+ "pbjson 0.8.0",
+ "prost 0.13.5",
  "serde",
 ]
 
@@ -2679,7 +2679,7 @@ dependencies = [
  "itertools 0.14.0",
  "object_store",
  "pbjson-types",
- "prost",
+ "prost 0.13.5",
  "serde_json",
  "substrait",
  "tokio",
@@ -3172,16 +3172,16 @@ dependencies = [
 name = "gen"
 version = "0.1.0"
 dependencies = [
- "pbjson-build",
- "prost-build",
+ "pbjson-build 0.8.0",
+ "prost-build 0.14.1",
 ]
 
 [[package]]
 name = "gen-common"
 version = "0.1.0"
 dependencies = [
- "pbjson-build",
- "prost-build",
+ "pbjson-build 0.8.0",
+ "prost-build 0.14.1",
 ]
 
 [[package]]
@@ -4447,6 +4447,16 @@ version = "1.0.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "57c0d7b74b563b49d38dae00a0c37d4d6de9b432382b2892f0574ddcae73fd0a"
 
+[[package]]
+name = "pbjson"
+version = "0.7.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c7e6349fa080353f4a597daffd05cb81572a9c031a6d4fff7e504947496fcc68"
+dependencies = [
+ "base64 0.21.7",
+ "serde",
+]
+
 [[package]]
 name = "pbjson"
 version = "0.8.0"
@@ -4457,6 +4467,18 @@ dependencies = [
  "serde",
 ]
 
+[[package]]
+name = "pbjson-build"
+version = "0.7.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6eea3058763d6e656105d1403cb04e0a41b7bbac6362d413e7c33be0c32279c9"
+dependencies = [
+ "heck",
+ "itertools 0.13.0",
+ "prost 0.13.5",
+ "prost-types 0.13.5",
+]
+
 [[package]]
 name = "pbjson-build"
 version = "0.8.0"
@@ -4465,22 +4487,22 @@ checksum = "af22d08a625a2213a78dbb0ffa253318c5c79ce3133d32d296655a7bdfb02095"
 dependencies = [
  "heck",
  "itertools 0.14.0",
- "prost",
- "prost-types",
+ "prost 0.14.1",
+ "prost-types 0.14.1",
 ]
 
 [[package]]
 name = "pbjson-types"
-version = "0.8.0"
+version = "0.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8e748e28374f10a330ee3bb9f29b828c0ac79831a32bab65015ad9b661ead526"
+checksum = "e54e5e7bfb1652f95bc361d76f3c780d8e526b134b85417e774166ee941f0887"
 dependencies = [
  "bytes",
  "chrono",
- "pbjson",
- "pbjson-build",
- "prost",
- "prost-build",
+ "pbjson 0.7.0",
+ "pbjson-build 0.7.0",
+ "prost 0.13.5",
+ "prost-build 0.13.5",
  "serde",
 ]
 
@@ -4735,6 +4757,16 @@ dependencies = [
  "unicode-ident",
 ]
 
+[[package]]
+name = "prost"
+version = "0.13.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2796faa41db3ec313a31f7624d9286acf277b52de526150b7e69f3debf891ee5"
+dependencies = [
+ "bytes",
+ "prost-derive 0.13.5",
+]
+
 [[package]]
 name = "prost"
 version = "0.14.1"
@@ -4742,7 +4774,27 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "7231bd9b3d3d33c86b58adbac74b5ec0ad9f496b19d22801d773636feaa95f3d"
 dependencies = [
  "bytes",
- "prost-derive",
+ "prost-derive 0.14.1",
+]
+
+[[package]]
+name = "prost-build"
+version = "0.13.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "be769465445e8c1474e9c5dac2018218498557af32d9ed057325ec9a41ae81bf"
+dependencies = [
+ "heck",
+ "itertools 0.14.0",
+ "log",
+ "multimap",
+ "once_cell",
+ "petgraph 0.7.1",
+ "prettyplease",
+ "prost 0.13.5",
+ "prost-types 0.13.5",
+ "regex",
+ "syn 2.0.113",
+ "tempfile",
 ]
 
 [[package]]
@@ -4758,13 +4810,26 @@ dependencies = [
  "once_cell",
  "petgraph 0.7.1",
  "prettyplease",
- "prost",
- "prost-types",
+ "prost 0.14.1",
+ "prost-types 0.14.1",
  "regex",
  "syn 2.0.113",
  "tempfile",
 ]
 
+[[package]]
+name = "prost-derive"
+version = "0.13.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8a56d757972c98b346a9b766e3f02746cde6dd1cd1d1d563472929fdd74bec4d"
+dependencies = [
+ "anyhow",
+ "itertools 0.14.0",
+ "proc-macro2",
+ "quote",
+ "syn 2.0.113",
+]
+
 [[package]]
 name = "prost-derive"
 version = "0.14.1"
@@ -4778,13 +4843,22 @@ dependencies = [
  "syn 2.0.113",
 ]
 
+[[package]]
+name = "prost-types"
+version = "0.13.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "52c2c1bf36ddb1a1c396b3601a3cec27c2462e45f07c386894ec3ccf5332bd16"
+dependencies = [
+ "prost 0.13.5",
+]
+
 [[package]]
 name = "prost-types"
 version = "0.14.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "b9b4db3d6da204ed77bb26ba83b6122a73aeb2e87e25fbf7ad2e84c4ccbf8f72"
 dependencies = [
- "prost",
+ "prost 0.14.1",
 ]
 
 [[package]]
@@ -5853,18 +5927,18 @@ dependencies = [
 
 [[package]]
 name = "substrait"
-version = "0.62.2"
+version = "0.58.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "62fc4b483a129b9772ccb9c3f7945a472112fdd9140da87f8a4e7f1d44e045d0"
+checksum = "de6d24c270c6c672a86c183c3a8439ba46c1936f93cf7296aa692de3b0ff0228"
 dependencies = [
  "heck",
- "pbjson",
- "pbjson-build",
+ "pbjson 0.7.0",
+ "pbjson-build 0.7.0",
  "pbjson-types",
  "prettyplease",
- "prost",
- "prost-build",
- "prost-types",
+ "prost 0.13.5",
+ "prost-build 0.13.5",
+ "prost-types 0.13.5",
  "protobuf-src",
  "regress",
  "schemars 0.8.22",
@@ -6271,7 +6345,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "66bd50ad6ce1252d87ef024b3d64fe4c3cf54a86fb9ef4c631fdd0ded7aeaa67"
 dependencies = [
  "bytes",
- "prost",
+ "prost 0.14.1",
  "tonic",
 ]
 
@@ -6428,9 +6502,9 @@ checksum = "f8c1ae7cc0fdb8b842d65d127cb981574b0d2b249b74d1c7a2986863dc134f71"
 
 [[package]]
 name = "typify"
-version = "0.5.0"
+version = "0.4.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e6d5bcc6f62eb1fa8aa4098f39b29f93dcb914e17158b76c50360911257aa629"
+checksum = "7144144e97e987c94758a3017c920a027feac0799df325d6df4fc8f08d02068e"
 dependencies = [
  "typify-impl",
  "typify-macro",
@@ -6438,9 +6512,9 @@ dependencies = [
 
 [[package]]
 name = "typify-impl"
-version = "0.5.0"
+version = "0.4.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a1eb359f7ffa4f9ebe947fa11a1b2da054564502968db5f317b7e37693cb2240"
+checksum = "062879d46aa4c9dfe0d33b035bbaf512da192131645d05deacb7033ec8581a09"
 dependencies = [
  "heck",
  "log",
@@ -6458,9 +6532,9 @@ dependencies = [
 
 [[package]]
 name = "typify-macro"
-version = "0.5.0"
+version = "0.4.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "911c32f3c8514b048c1b228361bebb5e6d73aeec01696e8cc0e82e2ffef8ab7a"
+checksum = "9708a3ceb6660ba3f8d2b8f0567e7d4b8b198e2b94d093b8a6077a751425de9e"
 dependencies = [
  "proc-macro2",
  "quote",
diff --git a/datafusion/ffi/Cargo.toml b/datafusion/ffi/Cargo.toml
index 28e1b2ee5681f..d5b0375565f0c 100644
--- a/datafusion/ffi/Cargo.toml
+++ b/datafusion/ffi/Cargo.toml
@@ -67,7 +67,7 @@ datafusion-proto-common = { workspace = true }
 datafusion-session = { workspace = true }
 futures = { workspace = true }
 log = { workspace = true }
-prost = { workspace = true }
+prost = { version = "0.13" }
 semver = "1.0.27"
 tokio = { workspace = true }
 
diff --git a/datafusion/functions/Cargo.toml b/datafusion/functions/Cargo.toml
index 2bdc05abe3806..7aadfefcc31e0 100644
--- a/datafusion/functions/Cargo.toml
+++ b/datafusion/functions/Cargo.toml
@@ -85,7 +85,7 @@ md-5 = { version = "^0.10.0", optional = true }
 num-traits = { workspace = true }
 rand = { workspace = true }
 regex = { workspace = true, optional = true }
-sha2 = { version = "^0.10.9", optional = true }
+sha2 = { version = "^0.10.8", optional = true }
 unicode-segmentation = { version = "^1.7.1", optional = true }
 uuid = { version = "1.19", features = ["v4"], optional = true }
 
diff --git a/datafusion/physical-expr/src/expressions/dynamic_filters.rs b/datafusion/physical-expr/src/expressions/dynamic_filters.rs
index 7703d201aaea9..643745ac0f07e 100644
--- a/datafusion/physical-expr/src/expressions/dynamic_filters.rs
+++ b/datafusion/physical-expr/src/expressions/dynamic_filters.rs
@@ -310,14 +310,14 @@ impl DynamicFilterPhysicalExpr {
     /// that created the filter). This is useful to avoid computing expensive filter
     /// expressions when no consumer will actually use them.
     ///
-    /// Note: We check the inner Arc's strong_count, not the outer Arc's count, because
-    /// when filters are transformed (e.g., via reassign_expr_columns during filter pushdown),
-    /// new outer Arc instances are created via with_new_children(), but they all share the
-    /// same inner `Arc<RwLock<Inner>>`. This is what allows filter updates to propagate to
-    /// consumers even after transformation.
+    /// # Implementation Details
+    ///
+    /// We check both Arc counts to handle two cases:
+    /// - Transformed filters (via `with_new_children`) share the inner Arc (inner count > 1)
+    /// - Direct clones (via `Arc::clone`) increment the outer count (outer count > 1)
     pub fn is_used(self: &Arc<Self>) -> bool {
         // Strong count > 1 means at least one consumer is holding a reference beyond the producer.
-        Arc::strong_count(&self.inner) > 1
+        Arc::strong_count(self) > 1 || Arc::strong_count(&self.inner) > 1
     }
 
     fn render(
diff --git a/datafusion/physical-plan/src/joins/hash_join/exec.rs b/datafusion/physical-plan/src/joins/hash_join/exec.rs
index 91fc1ee4436ee..f1c365c98434d 100644
--- a/datafusion/physical-plan/src/joins/hash_join/exec.rs
+++ b/datafusion/physical-plan/src/joins/hash_join/exec.rs
@@ -513,10 +513,8 @@ impl HashJoinExec {
     ///
     /// This method is intended for testing only and should not be used in production code.
     #[doc(hidden)]
-    pub fn dynamic_filter_for_test(&self) -> Option<Arc<DynamicFilterPhysicalExpr>> {
-        self.dynamic_filter
-            .as_ref()
-            .map(|df| Arc::clone(&df.filter))
+    pub fn dynamic_filter_for_test(&self) -> Option<&Arc<DynamicFilterPhysicalExpr>> {
+        self.dynamic_filter.as_ref().map(|df| &df.filter)
     }
 
     /// Calculate order preservation flags for this hash join.
diff --git a/datafusion/proto-common/Cargo.toml b/datafusion/proto-common/Cargo.toml
index c67c8892a3ded..a5618e1627384 100644
--- a/datafusion/proto-common/Cargo.toml
+++ b/datafusion/proto-common/Cargo.toml
@@ -45,7 +45,7 @@ json = ["serde", "pbjson"]
 arrow = { workspace = true }
 datafusion-common = { workspace = true }
 pbjson = { workspace = true, optional = true }
-prost = { workspace = true }
+prost = { version = "0.13" }
 serde = { version = "1.0", optional = true }
 
 [dev-dependencies]
diff --git a/datafusion/proto/Cargo.toml b/datafusion/proto/Cargo.toml
index b00bd0dcc6bfd..d86c1d70b35ac 100644
--- a/datafusion/proto/Cargo.toml
+++ b/datafusion/proto/Cargo.toml
@@ -68,7 +68,7 @@ datafusion-physical-plan = { workspace = true }
 datafusion-proto-common = { workspace = true }
 object_store = { workspace = true }
 pbjson = { workspace = true, optional = true }
-prost = { workspace = true }
+prost = { version = "0.13" }
 serde = { version = "1.0", optional = true }
 serde_json = { workspace = true, optional = true }
 
diff --git a/datafusion/substrait/Cargo.toml b/datafusion/substrait/Cargo.toml
index 8bfec86497ef0..0cb7e39a91974 100644
--- a/datafusion/substrait/Cargo.toml
+++ b/datafusion/substrait/Cargo.toml
@@ -41,9 +41,9 @@ datafusion = { workspace = true, features = ["sql"] }
 half = { workspace = true }
 itertools = { workspace = true }
 object_store = { workspace = true }
-pbjson-types = { workspace = true }
-prost = { workspace = true }
-substrait = { version = "0.62", features = ["serde"] }
+pbjson-types = { version = "0.7" }
+prost = { version = "0.13" }
+substrait = { version = "0.58", features = ["serde"] }
 url = { workspace = true }
 tokio = { workspace = true, features = ["fs"] }
 uuid = { version = "1.19.0", features = ["v4"] }
diff --git a/datafusion/substrait/src/extensions.rs b/datafusion/substrait/src/extensions.rs
index 0f848270babb9..b2b159dbf7799 100644
--- a/datafusion/substrait/src/extensions.rs
+++ b/datafusion/substrait/src/extensions.rs
@@ -115,13 +115,11 @@ impl TryFrom<&Vec<SimpleExtensionDeclaration>> for Extensions {
 impl From<Extensions> for Vec<SimpleExtensionDeclaration> {
     // Silence deprecation warnings for `extension_uri_reference` during the uri -> urn migration
     // See: https://github.com/substrait-io/substrait/issues/856
-    #[expect(deprecated)]
     fn from(val: Extensions) -> Vec<SimpleExtensionDeclaration> {
         let mut extensions = vec![];
         for (f_anchor, f_name) in val.functions {
             let function_extension = ExtensionFunction {
                 extension_uri_reference: u32::MAX,
-                extension_urn_reference: u32::MAX,
                 function_anchor: f_anchor,
                 name: f_name,
             };
@@ -134,7 +132,6 @@ impl From<Extensions> for Vec<SimpleExtensionDeclaration> {
         for (t_anchor, t_name) in val.types {
             let type_extension = ExtensionType {
                 extension_uri_reference: u32::MAX, // https://github.com/apache/datafusion/issues/11545
-                extension_urn_reference: u32::MAX, // https://github.com/apache/datafusion/issues/11545
                 type_anchor: t_anchor,
                 name: t_name,
             };
@@ -147,7 +144,6 @@ impl From<Extensions> for Vec<SimpleExtensionDeclaration> {
         for (tv_anchor, tv_name) in val.type_variations {
             let type_variation_extension = ExtensionTypeVariation {
                 extension_uri_reference: u32::MAX, // We don't register proper extension URIs yet
-                extension_urn_reference: u32::MAX, // We don't register proper extension URIs yet
                 type_variation_anchor: tv_anchor,
                 name: tv_name,
             };
diff --git a/datafusion/substrait/src/logical_plan/producer/expr/mod.rs b/datafusion/substrait/src/logical_plan/producer/expr/mod.rs
index 5057564d370cf..8a601bb4b84c9 100644
--- a/datafusion/substrait/src/logical_plan/producer/expr/mod.rs
+++ b/datafusion/substrait/src/logical_plan/producer/expr/mod.rs
@@ -62,7 +62,6 @@ use substrait::version;
 /// message.  The field names of the input schema will be serialized.
 // Silence deprecation warnings for `extension_uris` during the uri -> urn migration
 // See: https://github.com/substrait-io/substrait/issues/856
-#[expect(deprecated)]
 pub fn to_substrait_extended_expr(
     exprs: &[(&Expr, &Field)],
     schema: &DFSchemaRef,
@@ -88,7 +87,6 @@ pub fn to_substrait_extended_expr(
         advanced_extensions: None,
         expected_type_urls: vec![],
         extension_uris: vec![],
-        extension_urns: vec![],
         extensions: extensions.into(),
         version: Some(version::version_with_producer("datafusion")),
         referred_expr: substrait_exprs,
diff --git a/datafusion/substrait/src/logical_plan/producer/plan.rs b/datafusion/substrait/src/logical_plan/producer/plan.rs
index 9396329f8d3e7..e015652a8f76c 100644
--- a/datafusion/substrait/src/logical_plan/producer/plan.rs
+++ b/datafusion/substrait/src/logical_plan/producer/plan.rs
@@ -26,7 +26,6 @@ use substrait::version;
 /// Convert DataFusion LogicalPlan to Substrait Plan
 // Silence deprecation warnings for `extension_uris` during the uri -> urn migration
 // See: https://github.com/substrait-io/substrait/issues/856
-#[expect(deprecated)]
 pub fn to_substrait_plan(
     plan: &LogicalPlan,
     state: &SessionState,
@@ -48,13 +47,11 @@ pub fn to_substrait_plan(
     Ok(Box::new(Plan {
         version: Some(version::version_with_producer("datafusion")),
         extension_uris: vec![],
-        extension_urns: vec![],
         extensions: extensions.into(),
         relations: plan_rels,
         advanced_extensions: None,
         expected_type_urls: vec![],
         parameter_bindings: vec![],
-        type_aliases: vec![],
     }))
 }