I have an D and a C?

I am a junior in high school. My overall GPA is a 3.5 and I haven’t taken SATs yet. I was looking into schools like Syracuse and San Diego State. I have all As and Bs with the exception of a 78 in Algebra 2 Honors and a 68 in Chemistry Honors. Will colleges automatically decline me considering my poor grades in these individual classes? Will I have a hard time getting into ANY college?

For SDSU, they admit by Eligibility index and major.
EI= (CSU GPA x800) + (SAT Math+ CR) or (CSU GPA x 200) + (ACT Comp x10)
Competitive EI’s are 4100+ for SAT and 1050+ for ACT.

CSU GPA calculator: http://www.csumentor.edu/planning/high_school/gpa_calculator.asp

First you need to calculate your CSU GPA at the end of Junior year. If you are in-state CA, you get up to 8 extra honors points for UC approved Honors/AP/IB or DE courses taken 10-11th grade and capped at 8 semesters… A D in an Honors or AP class will not give you the extra points. If you go to a CA HS, you can look up your HS and which courses meet the criteria for the Honors points here:

https://hs-articulation.ucop.edu/agcourselist#/list/search/institution

If you do not attend a CA HS and are out of state, then only AP/IB/DE coursed taken 10-11th count for the extra points and grades have to be C or above.

You also have to meet the a-g course requirements for the Cal states which are listed below:

http://www.ucop.edu/agguide/a-g-requirements/

Again a D or below may not fulfill the a-g course requirements except for Math and Foreign Language. You can use validation by taking a higher level of Math or Foreign language to validate the D or lower grade. However, unless you repeat the exact course, that low grade (D or F) will be calculated in to your CSU GPA.
What are your other grades like? Plug what you have so far into the calculator to give you an idea of your chances.