For clarity may we contract that to “Emissions with… eutrophying effects were… reduced with the ICSs but not with the biogas system, due to emissions from… the digester”?
Either way, if “due to” could just as easily read “because of” then yes, it is appropriately used and the comma does add clarity.
Elegance is a different question. Here, it wold be more elegant to split the passage into two sentences, replacing “… system, due to…” with “… system. This was due to…”
Elegance also notices that “due to emissions from slurry storage and biogas leakages from the digester" is not at all unambiguous. Are there two different factors, the first emissions from slurry storage and the second biogas leakages from the digester? Do both come from the digester or what, please?