Aiming for graduate school in applied math with weak math grades I am close to finishing a degree in a combined program in computer science and physics, and I am thinking of applying to graduate school in environmental modelling, ideally with a strong mathematical and computational focus.

My overall GPA seems to be respectable, 3.72 (if I'm doing the conversion correctly). However, I have done much better in computer science courses (3.96) and worse in math (3.51) and physics (3.58).

The problem is that many of the grad programs I'm interested in are in math departments, and I fear that the low math GPA will exclude me from top programs. I should note that part of the reason for the math marks is that I took mostly honours courses, but I worry that admissions committees will not be able to tell (the course names don't always indicate this). I have, however, taken several courses in mathematical methods (both under computer science and math departments) and done very well, and am also taking a math-heavy graduate course in machine learning.

I have extended my degree by a semester to do a math minor, but unfortunately most of my marks for this will not be out by the time I apply for grad programs. I plan to study quite a bit for the GRE Math Subject Exam.

I have research experience in mathematical biology as well as currently working on an undergraduate thesis in environmental modelling. I will hopefully have one or two publications related to this research by the time I apply for schools.

How can I tailor my applications to have a good chance of getting into applied math programs? Will they care about my strong computer science marks, or my marks in specific courses? Should I try instead for computer science programs and go from there?
Your situation might be better than you expect. I'm in a math Ph.D. program with many faculties doing applied math research. My overall undergraduate GPA and math GPA were both worse than yours for similar reasons(e.g. a C+ in honor real analysis). In addition I have other unfavorable factors in my applications.

In the end you'll have to decide what programs to apply, here I assume you want to get into math/applied math program and you are concerned about your grade.

One of the reasons people look at your grade is to make sure you can pass through the coursework/qualifying stage of the graduate program. That is, they don't want to admit many students that will eventually drop out by failing too many courses or qualifying exams. To convince them you can do well in that part, you should


Get high subject GRE grade.
If your low math grade is on early stage and you do better after that(e.g. I got C+ in my first real analysis and A in my second real analysis course) then in SOP mention you understand the importance of those core courses and you work hard to make up the deficiency early on.
Related to 2. but more important, for any program you apply, take a look at all their requirements to graduate, and think about how you convince professors you will be able to finish those requirements.