My watershed has several big lakes. When I delineated my watershed, I had some unwanted subwatersheds and river segments inside the lakes (see fig. below). I want to tell ArcGIS/ArcHydro to delineate my watershed but ignore places where there are lakes/reservoir. Moreover, the generated subwatershed and streams should be consistent in terms of cascading flow from upstream to downstream e.g. subwatershed 2 flows to the lake and water from the lake flows to subwatershed 3, etc.

Any suggestion would be highly appreciated. Thanks!

Left: DEM with lakes; Right: Generated subwatershed with strange river shapes across the lake

  • Did you try using the Fill tool to fill sinks in the DEM?
    – Wes
    May 4, 2013 at 3:30
  • If you have only a few lakes it may be quicker to go into edit mode and merge those "lake watershed" polygons. But looking at your image those "lake watersheds" encompass more than just the lake itself, they include the adjacent land, what were your going to do with those?
    – Hornbydd
    May 5, 2013 at 20:37
  • Thanks Hornbydd! If ArcHydro can somehow take into account the lakes, the only option I can think of right now for adjacent land is to merge them with other subwatershed near by
    – samphilips
    May 6, 2013 at 20:47
  • @Wes: I did that already but it didn't help. Thanks anw
    – samphilips
    May 6, 2013 at 22:46

2 Answers 2


You will need to define your lakes as sinks (Create sink structures), and then use the ArcHydro function Adjust flow in lakes/streams/sinks. (These functions are only available in ArcHydro for ArcGIS 10.1, I have made a function that, with some modifications, might help you on the way if you are in 10.0.)

You can also erase (Extract by mask) the lakes from the raster (get Null values there) to accomplish the same thing, but that'll make it a bit harder to include the water flowing through the sinks/lakes in the end (if water volume is important to your analysis).

Workflows for 10.1, suggested by the ArcHydro team, can be found here.

  • Thank you very much for the reply, Martin! I'm using ArcGIS 10. I'll give 10.1 a shot!
    – samphilips
    May 6, 2013 at 20:42

This is a very interesting question. In general, there are two different types of lakes, endorheic and endorheic. So I am not sure how Arc Hydro handles them. There is a nice paper on this topic: Automatic watershed delineation in the Tibetan endorheic basin: A lake-oriented approach based on digital elevation models

But my concerns is if we use fill before flow direction, we will change the elevation around lakes and then that causes problem. Unless the "fill" algorithm can consider two different types of lakes as well.

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