I assume you have finished your qualification(s) and cannot try to get better marks in future subjects.
Is there anything I can do about [low marks on the transcript]?
Yes and no. While you should never alter your marks or misrepresent your experience and achievements, there is no reason why you cannot emphasize other areas instead. Many organizations hiring graduates are increasingly looking beyond your academic marks because they are not a great indicator of professional success. Instead, they are looking to your qualities as an individual. The ability to focus on a goal, work hard and stand out can count as much as good marks.
For example, you mention triathlon training. Were you successful? If so include that in your CV. It will generate interest and make you stand out from other candidates. Your interviewers might also be triathletes or otherwise athletic and it could be a great talking point.
It can be also great for those "behavioral" questions, such as "Tell me about a time when you really had to push yourself to achieve something?" (the last mile of the bike leg) or "Tell me about a leader you respect. What makes him/her great?" (talking about your coach). Did you mentor or help other triathletes? Did you interact with people from different backgrounds and you had to work together to get along? Did you do any fund raising or awareness? How did you (or your peers) cope with injury and diet? Did it help you with juggling different commitments (e.g. time management and prioritization)?
Should I say something in the cover letter?
Unless the hiring organization has specifically requested it, I would not mention your marks in your cover letter. Defending or explaining it will only draw attention to it. Say "academic transcript available on request", instead. Once you get a year or two of professional experience, your academic transcript becomes almost meaningless, anyway.
Similarly, try to relate non-academic experiences to the requirements in the job advertisement. For example, companies often require things like "works well under pressure" or "can work independently". Your non-academic experience should give you many and varied experiences to draw on. Focus on these in the cover letter.