How to Fix Invalid Geometry Errors in QGIS

Introduction

When you run a Processing tool such as clip or spatial join in QGIS, processing sometimes stops with an “invalid geometry” error.

This error means there is a problem with the shape of the data. If you leave it as it is, processing keeps failing, other GIS software may not read the data correctly, and the data may draw in unintended ways.

This article explains what an invalid geometry is, when it causes problems, and how to check and fix it in QGIS.

Processing fails to run

Processing tools such as clip and spatial join may stop with a message like Feature (...) has invalid geometry. Please fix the geometry or change the “Invalid features filtering” option for input layers or globally in Processing settings.

For example, the figure below shows the assumed flood inundation area data from the National Land Numerical Information Download Service, together with polygon data for Osaka City only, extracted from the administrative area data.

Run Clip with the flood inundation area data as the Input layer and the Osaka City polygon as the Overlay layer. An error appears as shown below and the processing fails.

This happens because the flood inundation area data used as the input layer contains features with problematic geometry.

Invalid geometries like these cause problems such as Processing tools failing to run.

What is an invalid geometry?

In vector data, the shapes of points, lines, and polygons are called “geometry.”

Geometries have shape rules that they must follow to be valid geospatial data. An invalid geometry is a shape that breaks those rules. Typical patterns include the following.

Polygon data

1. Self-intersection: The boundary of the polygon crosses itself.
2. Inner ring crosses the outer ring: A hole (inner ring) pokes through the outer boundary.
3. Zero-area polygon: The polygon has only two vertices, or some or all of its vertices lie on one straight line.

Line data

1. Zero-length line: The line consists of only a start point and an end point, and both are at the same location.

Invalid geometries like these can appear unintentionally while you create or edit data.

Check geometry validity with the Topology Checker

To check for invalid geometries, use the Topology Checker. Right-click the toolbar area and check Topology Checker Panel. The panel appears on the right side of the QGIS window.

First, configure the Topology Checker.

1. Click the Configure button in the Topology Checker panel.
2. Select the layer to check.
3. Select the rule to check. To check for geometry errors, select must not have invalid geometries.
4. Click the + button to add the rule.
5. Click OK.

Next, run the check.

1. Click Validate All. QGIS validates the layer against the rules you set.
2. If QGIS finds errors, it lists the affected features. Click an item to zoom the map to that feature.
3. Check Show errors on the canvas to highlight the features with errors on the map. This can make individual errors harder to see, so turn it on and off as needed.

Checking geometry validity and fixing invalid geometries early keeps your data quality high and prevents processing failures caused by data defects.

How to fix invalid geometries

You can fix the features with errors one by one by hand in edit mode, but this takes time when many features have errors. This section shows how to fix the errors automatically.

In the Processing Toolbox, run Vector geometry → Fix geometries.

1. Input layer: Select the layer whose geometries you want to fix.
2. Repair method: Choose the method used to repair the geometries. Structure prioritizes the correctness of the topological structure and fixes geometries more strictly. Linework prioritizes the original appearance and fixes geometries more leniently. If you are unsure, start with the default, Structure.
3. Fixed geometries: Specify where to save the fixed layer.

When the processing finishes, QGIS outputs a layer with the errors fixed.

Check the output layer with the Topology Checker in the same way as before. No errors are detected, which shows that the invalid geometries are resolved.

Now run Clip again with the repaired data. It failed with an error earlier, but this time the processing runs without problems.

Ignore features with invalid geometries and continue processing

Instead of repairing the geometries, you can also ignore the features with invalid geometries and continue processing. However, this method excludes the features with invalid geometries from the output, so use it with care.

From the menu bar, choose Settings → Options, then select the Processing tab on the left. Open Providers → General and change Invalid features filtering to Skip (ignore) features with invalid geometries.

With this setting, Processing skips features with invalid geometries and continues.

Conclusion

Invalid geometries can appear while you create or edit data. If you leave them as they are, Processing tools fail to run and other systems cannot read the data correctly.

So before an important analysis, before delivering data, or before exporting data for another system, run a topology check to make sure there are no problems.

If you find errors, deal with them using Fix geometries or the geometry editing tools.

Data sources

• “National Land Numerical Information (Administrative Area Data)” (Ministry of Land, Infrastructure, Transport and Tourism)
• “National Land Numerical Information (Assumed Flood Inundation Area Data)” (Ministry of Land, Infrastructure, Transport and Tourism)