diff --git a/python/sdist/amici/sbml_import.py b/python/sdist/amici/sbml_import.py
index a26c6e7d4a..8891055c1c 100644
--- a/python/sdist/amici/sbml_import.py
+++ b/python/sdist/amici/sbml_import.py
@@ -561,9 +561,9 @@ def _build_ode_model(
         assert dxdt.shape[0] - len(self.symbols[SymbolId.SPECIES]) == len(
             self.symbols.get(SymbolId.ALGEBRAIC_STATE, [])
         ), (
-            self.symbols[SymbolId.SPECIES],
+            self.symbols.get(SymbolId.SPECIES),
             dxdt,
-            self.symbols[SymbolId.SPECIES],
+            self.symbols.get(SymbolId.ALGEBRAIC_STATE),
         )
 
         # correct time derivatives for compartment changes
@@ -954,6 +954,7 @@ def _process_species(self) -> None:
             }
 
         self._convert_event_assignment_parameter_targets_to_species()
+        self._convert_event_assignment_compartment_targets_to_species()
         self._process_species_initial()
         self._process_rate_rules()
 
@@ -1564,6 +1565,36 @@ def _convert_event_assignment_parameter_targets_to_species(self):
                 "dt": sp.Float(0),
             }
 
+    def _convert_event_assignment_compartment_targets_to_species(self):
+        """Find compartments that are event assignment targets and convert
+        those compartments to species."""
+        for event in self.sbml.getListOfEvents():
+            for event_assignment in event.getListOfEventAssignments():
+                if event_assignment.getMath() is None:
+                    # Ignore event assignments with no change in value.
+                    continue
+                variable = symbol_with_assumptions(
+                    event_assignment.getVariable()
+                )
+                if variable not in self.compartments:
+                    continue
+                if variable in self.symbols[SymbolId.SPECIES]:
+                    # Compartments with rate rules are already present as
+                    # species
+                    continue
+
+                self.symbols[SymbolId.SPECIES][variable] = {
+                    "name": str(variable),
+                    "init": self.compartments[variable],
+                    # 'compartment': None,  # can ignore for amounts
+                    "constant": False,
+                    "amount": True,
+                    # 'conversion_factor': 1.0,  # can be ignored
+                    "index": len(self.symbols[SymbolId.SPECIES]),
+                    "dt": sp.Float(0),
+                }
+                del self.compartments[variable]
+
     @log_execution_time("processing SBML events", logger)
     def _process_events(self) -> None:
         """Process SBML events."""