I plan on taking online summer courses to improve some freshman grades (junior right now). When I apply to colleges and report grades, will colleges know that I took summer courses to improve some of the grades?
It likely depends on your high school. Does your high school replace poor grades with the ones you get in the summer, average the two, report both? The person who can best answer this is your high school guidance counselor. Ask if it will appear on your transcript for college apps. Keep in mind too that there are perhaps more worthwhile things to be doing with your summer if your grades weren’t that poor.
There are many colleges that will re-calculate your GPA without freshman year grades for admissions. If your school will report prior scores and you think it will substantially hurt your chances then consider applying to some of these schools.
You can tell them on your application only if you choose to.