Doubts when looking for possible PhD supervisors I'm currently in my last year of my master in environmental engineering and I'm strongly thinking about doing a PhD afterwards.  

I'm looking around for possible supervisors working with research topics that I'm interested in (especially micropollutants removal from water), but I don't know how to assess their and their research group reputation. What would be the best method to assess that?   

Also how early is it acceptable to send an email to inquire about a possibility to conduct a PhD project with them, especially if they work in a different university and thus know nothing about you?
To know about a research group reputation, you have to follow their research works (most likely that there will be a dedicated webpage for their group which lists their works). If it is not a research group then you have to shortlist a few professors and visit their webpages to know more about their works.

Now, before emailing anybody, you have to come to a decision point and zero in on few works that they have published or are working on. This will give you a focus area. Further, you have to understand them a bit and if you find them too much intriguing then you should email them.

Further questions on how to email professors can be browsed in academia SE.