How much does the ranking of your Master's program/school matter when applying to PhD programs? I'm applying for research-based Masters in Oceanography. So far, I've lined up advisors at University of Massachusetts (an intercampus program), South Florida, Georgia, and New Hampshire.  According to here,they are in top 150 globally for oceanography. Moreover, my current work supervisor says 3/4 are well-known.

I've also been talking to a UCSD prof. He told me he is unsure if he will be taking on students but is more inclined to accept a PhD student (since they'd be with him longer). I would really like to go to UCSD for my PhD.

Will going to a lower ranked MS have a big effect on PhD applications?

What can I do to distinguish myself in PhD application 1.5 or 2 years from now should the MS be low rank?
Don't get hung up on the ranking thing because it doesn't really matter when it comes to a PhD admission.  Top things that make your application stronger are


Skills you gained during MS and prior education/work experience
Letters of recommendation (high impact)
Writing sample (usually your statement of purpose/intent)
Willingness to learn new things
Your vision for a future career


That being said, try to find a program (either MS or PhD) that is best suited to your interests and that has the faculty expertise for you to learn from.