So I am currently pursuing my degree in Environmental Engineering and this is my question. What subjects/ skills do I really need to know really well?

It depends on the field you want to go into.  As an Environmental Engineer there are several opportunities, Mining, Oil and Gas, Water Infrastructure, Stormwater, Geotechnical, Remediation, etc.  I would make sure you have a solid understanding of geology and geological engineering so you have a good idea about how our environment was developed; how things (water, contaminants, etc) can move through that environment; what influences this; if you are developing it, how do you harness it; and if it is contaminated, how do you clean it up.  I would highly recommend you try a couple different internships to determine where your interests are.