diff --git a/src/mol-model/structure/query/queries/modifiers.ts b/src/mol-model/structure/query/queries/modifiers.ts
index e736b62fc..a0a9b5c45 100644
--- a/src/mol-model/structure/query/queries/modifiers.ts
+++ b/src/mol-model/structure/query/queries/modifiers.ts
@@ -545,6 +545,12 @@ export function surroundingLigands({ query, radius, includeWater }: SurroundingL
                     continue;
                 }
 
+                // Water is handled exclusively by the `includeWater` 3D-lookup branch below.
+                // A single water pulled in via a struct_conn metalc/covale edge would
+                // otherwise match every other water in the chain (all share label_seq_id
+                // and label_comp_id) and leak the entire chain.
+                if (StructureProperties.entity.type(l) === 'water') continue;
+
                 residuesIt.setSegment(chainSegment);
                 while (residuesIt.hasNext) {
                     const residueSegment = residuesIt.move();
diff --git a/src/servers/model/CHANGELOG.md b/src/servers/model/CHANGELOG.md
index fc3c98925..395c69d28 100644
--- a/src/servers/model/CHANGELOG.md
+++ b/src/servers/model/CHANGELOG.md
@@ -1,5 +1,6 @@
 # 0.9.13
 * /surroundingLigands: honor `omit_water=true|false` for REST GET requests (boolean parser previously coerced both to `false`)
+* /surroundingLigands: stop leaking the asymmetric unit's water chain into the result when `omit_water=true` (water residues pulled in via struct_conn covale/metalc edges no longer match every other water in the chain)
 
 # 0.9.12
 * add `health-check` endpoint + `healthCheckPath` config prop to report service health