1.ON TOPIC:
If you are going to use the clause it has a more irregular boundary as the direct object of assuming, you may not omit the subject of that clause.
However, you may omit the subordinating conjunction that:
An object is taken as a water feature, assuming it has a more irregular boundary.
Consequently, if you omit it while including that, that will be understood not as a conjunction but as a demonstrative pronoun: the subject of the clause.
An object is taken as a water feature, assuming that (water feature) has a more irregular boundary.
2.OFF TOPIC:
Your use of assuming may be is misleading. You should use assume only of facts which are not evident or given. However, from the tenor of your previous questions, and from your subordination of the assumption, I suspect that what you are dealing with here is an object which you observe to have an irregular boundary, from which you infer that it is a water feature. In that case, what you mean is:
An object with a more irregular boundary is assumed to be a water feature.
Your sentence would be correct only if what you mean is that when you know an object is a water feature, you assume that it has a more irregular boundary, and depict it accordingly.