Good Day:
I haven't thoroughly weighed out the evidence whether we have a negative effect of the reef environment but I believe we affect the environment.
I believe the biggest effects to the reef environment are overfishing, pollution (including agricultural runoff) and climate change.
For a look at the change of the ocean environment and tropical reefs the Netflix documentary "Mission Blue" documents the change of several reefs over 40 years.
http://www.imdb.com/title/tt2004304/?ref_=fn_al_tt_1
Michael