Be it endurance training or strength conditioning, exercise is not without a fair amount of aches and soreness. And of course, we wouldn't be human if we didn't think of ways we could ease any discomfort. After all, only a few steps to the medicine cabinet separate us from fast relief.

But what seems right in the moment may not be the best option long-term, especially if you're reaching for pain relievers — specifically anti-inflammatories like ibuprofen or naproxen — for otherwise normal and expected muscle soreness from workouts, according to Dr. Jonathan Zalamea, a primary care sports medicine physician at Houston Methodist. In fact, select ones may "dampen" your body's healing response or "numb" an actual injury, he says.

"Inflammation is a process the body uses to help repair, recover and protect itself," says Dr. Zalamea. "If you're sick, your body produces inflammation to help fight the infection. After workouts, the body uses inflammation to try and heal and rebuild the muscles back stronger."

"If someone's muscle soreness isn't causing a significant amount of discomfort to where they can't function, and it just hurts a bit, I tend to advocate not to use anti-inflammatories, so the body to recover on its own," he says.

Whatever your exercise level, Dr. Zalamea offers insight into the science behind soreness, differences between aches and injuries, options for relief (if you choose), and healthy habits to lessen soreness and the likelihood of injuries.

What causes sore muscles after a workout?

"Whether you're focusing on distance, speed or strength, you're going to get some soreness due to muscle breakdown," says Dr. Zalamea. "As you're doing these exercises, doing more reps or lifting heavier weight, you're pushing beyond the muscle what it's used to. The muscles are going to tear, but the expectation is that they rebuild back stronger."

These microscopic muscle tears are what triggers your body's inflammatory response and causes soreness a day or two after you've worked out — a phenomenon referred to as delayed onset muscle soreness (DOMS). Dr. Zalamea says with quality hydration, sleep and recovery, muscle soreness should improve over the course of a few days.

(Related: Can DOMS Be Prevented?)

What's the best pain reliever for sore muscles before, during or after workouts?

If you're just experiencing mild discomfort due to sore muscles, Dr. Zalamea tends to advocate for the "most natural route" possible and allow for the body to recover on its own without the use of medications or supplements.

If you feel you need help, Dr. Zalamea typically recommends that instead of NSAIDs like aspirin or ibuprofen, his patients take acetaminophen for occasional pains after workouts. It has fewer effects on the kidneys when a lack of proper hydration can be a risk factor due to sweating and loss of electrolytes.

NSAIDs can also interact with common blood pressure medications like diuretics to negatively impact kidney function, and ultimately could even lead to acute kidney failure. In addition, NSAIDs and diuretics may increase your sensitivity to sunlight.

The takeaway? You should consult with your doctor before any NSAID use — regardless of exercise — to make sure they're safe to take based on your health.

Lidocaine, an anesthetic that comes in creams or gels over the counter, is also something athletes may use to relieve localized pains like in the lower back or knees. The problem, Dr. Zalamea says, is lidocaine "simply numbs" the pain rather than addressing the root cause. You should also consult your doctor before any routine use of it, he says.

How do I know if it's 'just soreness' or a more serious injury?

"If you're not able to fulfill your day-to-day tasks, run as fast as you're used to, or your form is compromised, I would see a sports medicine doctor for further evaluation to see if it's truly 'just soreness' or a more serious injury," Dr. Zalamea says.

Muscle strains, ligament (connective tissue) sprains and stress fractures are all examples of exercise-related injuries that typically need more than rest alone to fully recover and should be examined by a sports medicine physician or practitioner.

"We not only focus on fixing the injury, but we also discuss ways we can prevent it from happening again, like proper diet, cross-training and form dynamics," he says.

(Related: The Difference Between Soreness and Serious Injuries)

7 habits that can help with sore muscles and injury prevention

Whether you're planning for a 5K, marathon or competition, injuries can prevent you from accomplishing your fitness goals. While sore muscles are inevitable and can be a sign of progress towards your goals, these healthy habits Dr. Zalamea offers can help you stave off sore muscles (without pain medication), prevent the likelihood of injury and achieve your goals.

Good hydration

With exercise, "hydration" isn't just water. It's a balancing act of replenishing what you've lost through sweat and exercise. That includes water, yes, but it also includes electrolytes like sodium and potassium that you can regain through options like sports drinks, electrolyte tablets or gels.

"I usually have long-distance athletes alternate between water and electrolyte drinks because water isn't enough, but exclusively drinking electrolyte beverages is too much," says Dr. Zalamea.

(Related: How to Stay Hydrated in the Heat)

Lessening workout intensity

"If ever you can't move from soreness, it probably means you pushed yourself too far and should dial your workouts back," says Dr. Zalamea. "I'm not saying stop working out, just dial it back, because your body needs to train up to get to that point your body was trying to do what you were asking from it."

Sufficient vitamin D

Forty-two percent of Americans are deficient in vitamin D, according to the National Institutes of Health. A lack of vitamin D can actually predispose the exercise enthusiast to stress fractures, says Dr. Zalamea. Sun exposure is a good way to get vitamin D, but you can also supplement what you need through foods fortified with vitamin D, like milk, grains or bread.

(Related: Is Vitamin D Deficiency a Silent Epidemic?)

Cross-training exercises

Cross-training is important for nearly any exercise regimen, whether that's a cardio sport like running or strength training. Not only does cross-training help strengthen the muscles you need to go further in your sport, it can also help prevent injuries from occurring. Examples of cross-training exercises include biking, swimming, weightlifting, yoga or Pilates.

Well-balanced diet

"A lot of times, you don't realize how many calories we burn when we're exercising, so making sure people get the adequate number of calories to fuel their workouts is important," says Dr. Zalamea.

A well-balanced diet contains a variety of fruits, vegetables, grains, fats and protein, but your specific ratios will vary depending on the intensity of your sport and training.

Adequate recovery

Your body needs rest, and overtraining can be a real possibility. Dr. Zalamea notes that recovery is a "big component of training" that a lot of people don't actually focus on. Recovery days can still be active — movements like walking, gentle stretching, foam rolling, and yoga are all considered "recovery" that can actually help reduce muscle soreness.

(Related: Tips for Proper Exercise Recovery)

Adequate sleep

Good sleep is important for everyone, but especially athletes, who require proper rest to repair their damaged muscles. Even for the busiest of athletes, it's recommended that adults get at least 7 hours of sleep nightly. Children and adolescents tend to need even more.