diff --git a/WDL/Type.py b/WDL/Type.py
index db8c0170..12739989 100644
--- a/WDL/Type.py
+++ b/WDL/Type.py
@@ -483,7 +483,7 @@ def coerces(self, rhs: Base, check_quant: bool = True) -> bool:
         return False
 
 
-def unify(types: List[Base], check_quant: bool = True, force_string: bool = False,) -> Base:
+def unify(types: List[Base], check_quant: bool = True, force_string: bool = False) -> Base:
     """
     Given a list of types, compute a type to which they're all coercible, or :class:`WDL.Type.Any`
     if no more-specific inference is possible.
@@ -496,20 +496,38 @@ def unify(types: List[Base], check_quant: bool = True, force_string: bool = Fals
 
     # begin with first type; or if --no-quant-check, the first array type (as we can try to promote
     # other T to Array[T])
-    t = types[0]
+    t = next((t for t in types if not isinstance(t, Any)), types[0])
     if not check_quant:
-        t = next((a for a in types if isinstance(a, Array)), t)
+        t = next((a for a in types if isinstance(a, Array) and not isinstance(a.item_type, Any)), t)
+    t = t.copy()  # pyre-ignore
 
     # potentially promote/generalize t to other types seen
     optional = False
     all_nonempty = True
     all_stringifiable = True
     for t2 in types:
+        # recurse on parameters of compound types
+        t_was_array_any = isinstance(t, Array) and isinstance(t.item_type, Any)
+        if isinstance(t, Array) and isinstance(t2, Array) and not isinstance(t2.item_type, Any):
+            t.item_type = unify([t.item_type, t2.item_type], check_quant, force_string)
+        if isinstance(t, Pair) and isinstance(t2, Pair):
+            t.left_type = unify([t.left_type, t2.left_type], check_quant, force_string)
+            t.right_type = unify([t.right_type, t2.right_type], check_quant, force_string)
+        if isinstance(t, Map) and isinstance(t2, Map):
+            t.item_type = (  # pyre-ignore
+                unify([t.item_type[0], t2.item_type[0]], check_quant, force_string),  # pyre-ignore
+                unify([t.item_type[1], t2.item_type[1]], check_quant, force_string),  # pyre-ignore
+            )
+        if not t_was_array_any and next((pt for pt in t.parameters if isinstance(pt, Any)), False):
+            return Any()
+
+        # Int/Float, String/File
         if isinstance(t, Int) and isinstance(t2, Float):
             t = Float()
         if isinstance(t, String) and isinstance(t2, File):
             t = File()
 
+        # String
         if (
             isinstance(t2, String)
             and not isinstance(t2, File)
@@ -520,9 +538,10 @@ def unify(types: List[Base], check_quant: bool = True, force_string: bool = Fals
         if not t2.coerces(String(optional=True), check_quant=check_quant):
             all_stringifiable = False
 
-        if t2.optional:
+        # optional/nonempty
+        if t.optional or t2.optional:
             optional = True
-        if isinstance(t2, Array) and not t2.nonempty:
+        if isinstance(t, Array) and not t.nonempty or isinstance(t2, Array) and not t2.nonempty:
             all_nonempty = False
 
     if isinstance(t, Array):
diff --git a/WDL/Value.py b/WDL/Value.py
index b47f07bd..9f5a285a 100644
--- a/WDL/Value.py
+++ b/WDL/Value.py
@@ -415,6 +415,12 @@ def from_json(type: Type.Base, value: Any) -> Base:
         return String(value)
     if isinstance(type, Type.Array) and isinstance(value, list):
         return Array(type, [from_json(type.item_type, item) for item in value])
+    if isinstance(type, Type.Pair) and isinstance(value, list) and len(value) == 2:
+        return Pair(
+            type.left_type,
+            type.right_type,
+            (from_json(type.left_type, value[0]), from_json(type.right_type, value[1])),
+        )
     if (
         isinstance(type, Type.Map)
         and type.item_type[0] == Type.String()
diff --git a/tests/test_0eval.py b/tests/test_0eval.py
index 84fe4114..b40a0fef 100644
--- a/tests/test_0eval.py
+++ b/tests/test_0eval.py
@@ -448,6 +448,7 @@ def test_json(self):
             (WDL.Type.Map((WDL.Type.String(), WDL.Type.Int())), {"cats": 42, "dogs": 99}),
             (pty, {"name": "Alyssa", "age": 42, "pets": None}),
             (pty, {"name": "Alyssa", "age": 42, "pets": {"cats": 42, "dogs": 99}}),
+            (WDL.Type.Array(WDL.Type.Pair(WDL.Type.String(), WDL.Type.Int())), [["a",0],["b",1]]),
 
             (WDL.Type.Boolean(), 42, WDL.Error.InputError),
             (WDL.Type.Float(), "your president", WDL.Error.InputError),
diff --git a/tests/test_1doc.py b/tests/test_1doc.py
index 7e20cbaf..de05c00a 100644
--- a/tests/test_1doc.py
+++ b/tests/test_1doc.py
@@ -490,9 +490,14 @@ def test_unify(self):
         workflow unify {
             String s
             File? f2
+            Array[Int] a1 = [1]
+            Array[Int?]? a2 = []
+            Array[Pair[String,String]] ap = [(0,1),(2,3)]
+            Array[Map[String,String]] am = [{ "a": 0, "b": 1 }, { "a": "x", "b": "y" }, { 1: 2, 3: 4 }]
 
             output {
                 Array[File?] a = [s, f2]
+                Array[Array[Int?]?] a3 = [a1, a2]
                 Map[String, File?] m = { "foo": s, "bar": f2 }
                 Map[Float, File?] m2 = { 1: s, 2.0: f2 }
             }
@@ -500,6 +505,14 @@ def test_unify(self):
         """)
         doc.typecheck()
 
+        with self.assertRaises(WDL.Error.ValidationError):
+            doc = WDL.parse_document("""
+            workflow unify {
+                Array[Pair[String,String]] bogus = [("a","b"), ("c",("d","e"))]
+            }
+            """)
+            doc.typecheck()
+
 class TestDoc(unittest.TestCase):
     def test_count_foo(self):
         doc = r"""#foo
diff --git a/tests/test_3corpi.py b/tests/test_3corpi.py
index 270c5a9b..64227fe4 100644
--- a/tests/test_3corpi.py
+++ b/tests/test_3corpi.py
@@ -300,7 +300,7 @@ class ViralNGS(unittest.TestCase):
 @wdl_corpus(
     ["test_corpi/ENCODE-DCC/chip-seq-pipeline2/**"],
     expected_lint={
-        "StringCoercion": 192,
+        "StringCoercion": 208,
         "FileCoercion": 154,
         "NameCollision": 16,
         "OptionalCoercion": 64,