Troubleshooting Coordinate Systems Issues
When working with GIS data, coordinate system issues are a frequent source of misaligned layers, missing features, or incorrect map displays. Understanding the root causes of these problems—and how to fix them—can save time and ensure spatial accuracy. This article helps GIS users understand how to troubleshoot misaligned data due to coordinate system issues and explains when to use Define Projection vs. Project. It is especially useful in workflows where spatial integrity is critical.
Common Coordinate System Issues:
Unknown Coordinate System
The dataset has no defined coordinate system. ArcGIS doesn’t know how to place the features on the map.
Incorrectly Defined Coordinate System
The coordinates themselves are correct, but the label (spatial reference) is wrong—for example, meters stored as if they were degrees.
Mismatched Coordinate Systems
Layers are in different spatial references, causing them to display in different locations or scales.
No Geographic Transformation Applied
When projecting data between different datums (e.g., NAD83 to WGS84), failing to apply a geographic transformation can cause subtle misalignments.
Inconsistent Map and Layer Coordinate Systems
The map's spatial reference differs from that of the layer, which can cause display anomalies or incorrect scale behavior.
Extent Values Don't Match the Labeled Units
The coordinate values (X/Y) suggest one system, but the software interprets them as something else—e.g., values like -180 or 34.5 used with a UTM or State Plane label.
1 – Understanding Coordinate Systems
Key Concepts:
- Geographic Coordinate Systems (GCS) use latitude/longitude (e.g., WGS 1984).
- Projected Coordinate Systems (PCS) flatten the Earth to a 2D surface (e.g., NAD 1983 UTM Zone 13N).
- Datum defines the size and shape of the Earth model (e.g., NAD 1983 vs. WGS 1984).
- All layers must be in the same coordinate system to align properly.
Please read this article for more: https://support.tribalgis.com/article/29-basics-of-coordinate-systems-and-projections
2 – Diagnosing Common Issues
- Symptom 1: Layers don’t line up
Possible Cause: One or more layers are missing a defined coordinate system or are defined incorrectly.
Check this by right clicking the layer > Properties > Source > Spatial Reference.
If you missed the ArcGIS Pro pop-up notification about an unknown coordinate system, you can find it again by clicking the notification bell icon in the top right corner of the interface, next to your username. This will show recent alerts, including warnings about undefined spatial references.
- Symptom 2: Data shows up in the wrong part of the world
Possible Cause: The coordinate system was defined incorrectly instead of reprojected.
3 – Don’t Trust the Units: Check the Extent Values
When diagnosing projections issues, don't just look at the coordinate system name - also check the extent values to catch mislabeled data. Even if the coordinate system name appears correct, the actual coordinate values (X, Y) might not make sense for that system — a classic sign of mislabeling.
Where to Look:
- Right-click the layer > Properties > Source > Extent tab.
In the example below, the range clearly suggests decimal degrees, but if the coordinate system is incorrectly labeled as UTM or State Plane, ArcGIS will interpret those same numbers as meters, placing your data far from where it belongs.
What This Tells you:
- The values in the extent are correct - they reflect how the data was originally recorded.
- The coordinate system label is wrong - ArcGIS thinks it's in meters when it's actually in degrees (or vice versa).
How to Fix it:
- Use the Define Projection tool to correct the label.
- After that, if needed, use the Project tool to convert the data into your desired coordinate system.
4 – Tools to Fix It
- Define Projection Tool
Use when a dataset has no spatial reference, but you know what it should be.
Important: This does not reproject coordinates — it only labels them correctly.
- Project Tool
Use when the dataset has the correct defined projection and you need to convert it to another one.
This creates a new dataset with transformed coordinates.
5 – Common Problems and How to Fix Them
Problem 1: Unknown Coordinate System
- Symptom: Layer shows up in the wrong place or doesn’t appear at all.
- Solution: Use the “Define Projection” tool to assign the correct coordinate system if you know it.
Problem 2: Mismatched Coordinate Systems
- Symptom: Two layers don’t align even though both have defined coordinate systems.
- Solution: Project one of the layers to match the coordinate system of the other using the “Project” tool.
Problem 3: Incorrect Coordinate System Label
- Symptom: Coordinate values suggest the data is in degrees, but the label says UTM (or vice versa).
- Solution: Reassign the correct spatial reference using “Define Projection”. Then use “Project” if needed.
Problem 4: Missing Geographic Transformation
- Symptom: Data looks slightly shifted after projection between datums (e.g., NAD 1983 to WGS 1984).
- Solution: Use a proper geographic transformation during the projection process. ArcGIS will suggest options.
Problem 5: Inconsistent Map and Layer Coordinate Systems
- Symptom: Data appears in the wrong area or scale when added to the map.
- Solution: Set the map’s coordinate system to match your main dataset or reproject layers accordingly.
Tips
- Always check the layer’s coordinate system via Properties > Source.
- Examine the layer’s Extent to confirm units make sense for that system.
- Use “Define Projection” only when the coordinate system is missing or mislabeled — not to reproject data.
We hope that this article has been helpful! If you have any feedback or questions, please feel free to send us an email or connect with us for a chat. The NTGISC team is here to assist you further!