Hydrological Analysis Using Whitebox Geospatial Analysis Tools

Introduction

This tutorial uses Whitebox tools, an open source GIS software that was developed within the Center for Hydrogeomatics in Guelph University. As a result this software package has a heavy focus on hydrological analysis. For this reason Whitebox was chosen for this tutorial on hydrological analysis. WhiteBox has recently been completely re-written from the ground up using a more advanced backend. This means that the toolset has migrated away from a stand-a-lone software. It is now accessible either through code (Python or R) or as a package using QGIS. This tutorial originally used the older version but has been updated to use the QGIS version in October 2026.

The area of focus in this tutorial is Calabogie Ontario. This location was chosen because the Calabogie peak adds some relief to the area, and the author knew it well enough to tell if there were any errors that occurred during the analysis process.

This tutorial uses a single input, a Digital Elevation model, and produces a multitude of outputs from it, adding information that could be used for future analysis. The process that will be undergone in this tutorial is displayed in the image below. To understand the context of each tool used in this tutorial please refer back to this image as needed.

Data Acquisition

In this tutorial the only necessary layer is a Digital Elevation Model (DEM) file of your area of interest. In this tutorial we are focusing on Calabogie, ON. It is recommended that you use tthis same dataset for following along.

It can be acquired and downloaded here.

A sample of this data is shown bellow.

For the event that the dropbox link has become inactive the process of obtaining this data is described below to make this tutorial relevant for longer.

Access the Government of Canada Geospatial Data Extraction Application here.

In the “Select Clipping Area” bar enter change the selection to "Predefined Clipping Area" and then select "Drainage areas" from the drop down list that appears.

This produces a long list of sequential drainage area names. Search through the names until you find "02KE000" and select it. I found this on the 17th page of drainage area names.

The map extent on the right side of the web page should now match the image below.

Under “Select Data to be extracted” Select “Elevation – Digital elevation model”.

Under “Select options and submit job” fill all of the required boxes so that it matches the figure below. Make sure to enter the email address that you would like to have the file sent to in the “Email Address” field.

An email will be sent to the entered email address shortly which contains a URL for the direct download of the data.

If neither of these options are available, any DEM raster can be used.

Acquiring and Installing Whitebox Plugin (QGIS)

Please note the previous version of Whitebox used for this tutorial is now deprecated and has transitioned to be used via coding APIs or QGIS only. This tutorial will now show the user how to use Whitebox Geospatial Analysis Tools in QGIS. This tutorial presumes the user has some QGIS knowledge and already has QGIS installed. For more details, please see the the QGIS download page for more instructions.

To setup your QIGS workspace for WhiteBox you will need to install the "WhiteBox Workflows for QGIS" plugin.

To start, find the plugin manager in QGIS by going to plugins > Manage and Install Plugins...

Then search all plugins for "WhiteBox Workflows for QGIS"

Getting Started

Import DEM into QGIS

Import the DEM you downloaded into QGIS by adding it as a layer. You can do this by finding the layer in the QGIS browser or simply dragging it from the directory into QGIS. If it correctly imported, you should see the DEM displayed on the screen.

Accessing WhiteBox Tools

You're now all set to start using WhiteBox Tools. If you do not see them go to Processing > Toolbox to display the window.

You will find the whitebox tools displayed at the bottom of the list. These tools will be used for the rest of the tutorial so please make sure you have access to them as shown here.

Hydrological Analysis

DEM Pre-Processing

Pre-processing is an important first step in any hydrological analysis as this process identifies and corrects all features within the DEM that may disrupt the flow analysis. Since all products are derived from the DEM it is important to make these corrections at the begging of the process to prevent these errors from carrying through into all of the hydrological outputs.

In this tutorial the "Fill Depressions" tool is used to hydrologically correct the DEM. This was chosen because it is much more computationaly efficient than any of the breach tools, finishing much quicker.

This tool is found in the location below.

The dialog box that appears for this tool is shown below. The input file should be set to the original Calabogie DEM.

The output of this tool is shown below. It does not appear very different to the original DEM, but will closer inspection differences within the areas identified in the Find No-Flow Cells output can be seen.

Flow Pointer

A flow pointer tool in Whitebox is a tool that identifies which area surrounding a cell is the lowest. The value of this cell is then assigned corresponding to the relative direction of this area. This information is not too useful on its own, but it is used as an input to many other hydrology tools because it denotes the direction that water will flow from each cell.

Whitebox has many different flow pointer tools that each use a different method to produce their results. In this tutorial "D8 Flow Pointer" was used because many of the tools in the "Watershed Tools" toolset will only work with the output from the D8 Flow Pointer as an input. This tool is found in the location shown below.

The dialog box for this too is shown below. The input DEM raster file should be set to the output from the Fill Depressions tool.

The output from this tool is displayed below. This image contained 8 colours corresponding to the 8 directions of flow. This image appears chaotic, but will be used in other tools to create more informative data products.

Flow Accumulation

Flow Accumulation tools analyze the magnitude of cells that pour into or through an area. This is useful on its own, allowing us to determine the relative flow through areas by comparing values of the output, and is also used as an input for many other analyses.

In this tutorial the "D8 Flow Accumulation" tool was used, as this was the one that corresponded to the D8 Flow Pointer output that was created with the previous tool. This tool is located in the location displayed below.

The dialog box for this tool is displayed below. The input D8 flow pointer raster file should be set to the output from the D8 flow pointer tool. In the example the "Output Type" was set to "cells" so that a greater cell value in the output would correspond to a greater number of cells flowing through that cell. The "Log-transformed flow accumulation values?" box was left unchecked in this example, though checking this would help normalize the data for better display. After these inputs have been set click "Run" in the bottom left of the popup window.

The output of this tool is displayed below. The brighter areas correspond to areas of higher accumulated flow. These areas of high flow correspond to the areas where more water gathers and flows together. A beter picture of the data can be gathered by zooming into the output in Whitebox.

Isobasin

The isobasin tool divides a study area into equally sized drainage areas (iso-basins) of a specified size.

The location of this tool is displayed below.

The dialog box for this tool is displayed below. The input is the original, hydrologically conditioned (depression fill) raster.

The output from this look is displayed below. It can be seen that the area has been broken down into 11 different basins of approximately equal size. It also appears that the basins do not fill the entire study area. This is likely because no more basins of a size of 500,000 cells could be fit into these areas. If the target basin size was set to a lower number these basins would conform to the study area more completely.

Extract Streams

Stream networks can be useful as an input for other tools. Also, on their own they allow knowledge of areas of high water and nutrient flow, as well as connecting areas between water habitats.

The "Extract Streams" tool was used for this purpose. This tool extracts all values from a flow accumulation output that are greater than the specified value. This tool is not located within the Hydrology Tools toolset, and is part of the "Stream Network Analysis" toolset instead. The location of this tool is displayed below.

The dialog box for this tool is displayed below. The input flow-accumulation raster file should be set to the output from the D8 and Rho8 Flow Accumulation (D8 and Rho8 Flow Accumulation), and the output should be set to the DataProducts folder and named something similar to "ExtractStreams.dep". The "Channelization Threshold" is the cutoff value that will be used to determine which cells are a stream and which cells aren't. Trial and error was used to determine a value that produced an appropriate stream network. A value of 50,000 was settled on. The "Background Value" was set to "NoData" so that all of the cells that were not streams would be transparent. After these inputs have been set click "Run" in the bottom left of the popup window.

The output of the tool is displayed below. This output looks patchy at the full extent, but by zooming into it within Whitebox you can confirm that a network of continuous lines has been produced.

Sub-basins

The sub-basin tool breaks the down the study area into a number of basins, with one basin for each segment of a stream network for the area. As a result each of these basins represent the catchment area for each segment of the river network.

The location of this tool is displayed below.

The dialog box for this tool is displayed below. The input streams raster file should be set to the output from the extract streams tool (ExtractStreams.dep), and the input D8 flow pointer raster should be set to the output from the D8 flow pointer tool (FlowPointer.dep). The output should be set to the DataProducts folder and named something similar to "Subbasins.dep". After these inputs have been set click "Run" in the bottom left of the popup window.

The output from this tool is displayed below. This image shows a much greater number of basins than any of the outputs from other tools in this tutorial, likely due to the complexity of the stream network fed into the tool. It would be expected that if the channelization threshold used for the extract streams tool was higher, there would be less sub-basins, and if it was lower there would be more.

Watershed Analysis

In order to run the Watershed tool this first step will be to create pour points. Once this is done The watershed analysis can be done.

Pour Points

Pour points are used in watershed analysis to define each of the watersheds that will be output. Simply put, a watershed is the entire area that flows into a pour point. As a result the placement of these pour points greatly effects the output of the watershed analysis. Pour points are usually located in areas of high accumulated flow, so are usually located on points of a stream network.

There is no way to create a pour point file in Whitebox automaticaly, so this must be done manualy. You can do this by creating a new point layer in QGIS. Go to layer > Create layer

You can create whichever data structure you prefer for vectors, for this tutorial we use a shapefile. Make sure to set your CRS to the same CRS as the pre-requisite hydrological products that have already been created. Then set the geometry type to Point. Your dialog box may look something like below.

Pour points must now be identified and added. Before this can be done, the layers in the data tab have to be set up. I made sure that only the extract streams output and the create blank outlet raster output were visible, and that only the create blank outlet raster output was highlighted in the layer list.

Next the vector layer must be edited tool, start by enabling editing like so.

You can then create points from here by first clicking on the 'Add Point Feature' button

After clicking this button your cursor will become a cross-hair when mousing over your data frame. The center of this cross-hair is the location of the pixel that will be altered using this tool.

Click on a location along the stream network, such as the location displayed below. When you click on it a small window like the one below will appear. This window tells you the co-ordinates of the pixel you are changing, and the current value of the pixel. The value should currently be NoData.

Change this value from NoData to 1.

Repeat this process until you are happy with the placement of your pour points, making sure that the value of each pour point is unique. For the example in this tutorial 10 pour points were spread evenly along the stream network and were given sequential values from 1 to 10.

It is important that the placement of these pour points is on the stream network, so the Jenson Snap Pour Points tool will now be used to make sure that this is true.

The location of this tool is displayed below.

The dialog box for this tool is displayed below. The input outlets file should be set to the output from the create blank outlet raster tool that you have just modified (OutletRaster.dep). The input streams raster should be set to the output from the extract streams tool (ExtractStreams.dep). The output should be set to the DataProducts folder and named something similar to "PourPoints.dep". After these inputs have been set click "Run" in the bottom left of the popup window.

After this you will get a new point layer that is perfectly snapped to the stream network. Use this point layer for future analysis instead of your manually created layer.

Watershed

Now that the pour point raster has been created and snapped to the stream network the watershed analysis can be undergone. The location of this tool is displayed below.

The dialog box for this tool is displayed below. The D8 flow pointer raster file should be set to the output from the D8 flow pointer tool (FlowPointer.dep). The pour point file should be set to the output from the Jenson snap pour points tool (PourPoints.dep). The output should be set to the DataProducts folder and named something similar to "Watershed.dep". After these inputs have been set click "Run" in the bottom left of the popup window.

The output of this tool is displayed below. This shows 10 watershed ares, corresponding to the locations that the pour points were located. Each of these watersheds also conserve the value that its pour point had, meaning that any hierarchy or numbering system will be kept.

The number and location of your watershed areas will differ as a result of the different pour points used.

Conclusion

This tutorial aimed to give the user in introduction to hydrological analysis using Whitebox GAT 3.4.0. This was done by taking the user through an organized process that linked many of the hydrology tools together and explained why they were used and how the parameters were decided for each one.

The user should now have a good basis of knowledge that will help them with future hydrological analysis in Whitebox Geospatial Analysis Tools.