"Alegaciones" are pleadings in court proceedings. You can also simply call them "arguments". Phil's "submissions" is also OK. I think "arguments submitted" on the Plan Hidrológico Nacional is how I would put it. This refers to the public debate on the PHN when interested parties were able to submit arguments on the Plan.

But why "Propuesta en alegaciones"? It's surely a very odd way of putting it, if what it means is simply a proposed submission. In fact I can't see a linguistic argument for that "en", on the face of it.

That is, until we look at the source (or at least, what I assume must be the source, to which I will not give a reference for obvious reasons).

The heading, as you say, is "Propuesta en alegaciones al Plan Hidrológico Nacional". The text of this section goes as follows:

"Propuesta en alegaciones al Plan Hidrológico Nacional (Prat, 2001)
Durante el proceso de discusión del Plan Hidrológico Nacional, en Prat (2001) se realiza una propuesta basada en las funciones ambientales de los caudales [...]"

So what it's talking about is a proposal that was put forward in a study by Prat. This, if we refer to the bibliography, is an essay published in a volume entitled El Plan Hidrológico Nacional a debate.

In other words, what I think it must mean is that the "alegaciones" (arguments) referred to are those Prat put forward in his article as part of the national debate. Those arguments contained a proposal, which is discussed in this section of your text. So it means a proposal (contained) in arguments submitted on the Plan Hidrológico Nacional, and the way it's formulated is perfectly logical: the problem with "en" disappears.

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Note added at 12 hrs (2016-08-24 21:52:27 GMT)
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So yes, it's to do with the public consultation process, in which this proposal emerged.