I want to analyze the interaction between fish abundance with environment variables. Does anyone have experience using subsurface data (sst, salinity, etc)? Where can I download this kind of data?
Download Ocean Data View (ODV) at odv.wi.de. It is a free software for ocean data analysis. It is very easy to use. The instructions shall tell you where to download the public domain data for your study site.
You can also use your own data files with the software.
I don't have many experiences but I think you can find subsurface data from WOCE (World Ocean Circulation Experimen - http://www.ewoce.org/) and use ODV or other programs (for netcdf files) to read.