You have a rather complex data set. it may help to examine it step by step and part by part. Have you tried any graphical work? It can help your thinking quite a bit. Take distance from aquaculture site on x axis and abundance of a species on y axis. Use different colors for different transects. Ask the following questions: does abundance increase with distance? Is this true for all 8 transects? If not, do transects fall in groups? you can go into further detail and ask how the comparative picture changes with distance from aquaculture. You should take up formal analysis only after data visualization gives you some insights. Admittedly, these are only suggestive and formal testing is needed. Here too, one omnibus model may not be the best way to attack the problem. Why not start with one continuous response (abundance of just one taxon) and see what you get? Even in case of categorical response, you could simply use the average of the range (12.5 instead of 1-25%).

Hi Mr. Gore and thank you for your input and suggestions. To answer your 1st point, yes there are maps of species abundances and you can see a decrease in some species (e.g. Beggiatoa-like bacteria) with distance from the aquaculture site and increase in others (e.g. anemones). 

For the record, after discussions with other colleagues, I believe since my species in categories (from 0 = absence to 4 = 75-100% cover) are somewhat already transformed, the best way will be square root transform my species abundances (already fairly low). This way all species (either in category or abundance) fall between 0 and 4 and have the same potential range and weight across the matrix. 

Your description of the graphs is interesting. since some bacterial like species have decreasing abundance as distance from aquaculture increases, it suggests that somehow those bacteria like species benefit from aquaculture. Can you say why? Similarly, some anemones increase in abundance as distance from aquaculture increases. Why is this so? Can you guess the answer? In each case, your guess should lead to further analysis or confirmation.

Hi Mr. Gore, yes previous studies showed that those bacteria are opportunistic and are found only around aquaculture sites, not at reference sites. As for anemones, maybe my last answer wasn't clear but we observe the opposite, they are absent around aquaculture site but start to appear as we move away from aquaculture. The fish feed and feces are the most likely causes of this change. I'm now doing the analyses to see how this affect the benthic communities and I should have more answers soon. 

Thank you for your input!