Swimming is an excellent exercise that is gentle on joints.

With regard to squats, I would definitely get a second opinion - generally, going to at least parallel is easier on the knees - however, your physical therapist has your specific medical issues and can examine you and as such I would go with what they say (assuming the PT second opinion concurs).

I would also ask them what lower body exercises you can do that will not put a strain on your knees - there are a lot of ones that can be done.

When you see the second PT, you may want to show them this extract from Mark Rippetoe's Starting Strength for discussion:

"Squats are not "bad for the knees". They are, in fact, good for the knees. Properly performed, they evenly and proportionately strengthen all muscles which stabilize and control the knee (in addition to strengthening the muscles of the hip and posterior chain, upper back, shoulder girdle, etc.). When the hips are lowered in a controlled fashion below the level of the top of the patella, full hip flexion has occurred, and this will activate the hamstrings and glutes. In doing so, the hamstrings are stretched at the bottom of the motion and they pull the tibia backwards (toward da' butt) which counteracts the forward-pulling force the quadriceps apply during the motion. As a result, the stress on the knee tendons is lessened since the hamstrings assist the patellar tendon in stabilization of the knee. A muscle supporting a tendon which supports the kneecap is going to be better than the tendon having to take up the entirety of the strain by itself..

Think about Olympic lifters. They squat VERY deep (almost ridiculously deep) all the time, frequently 5 or 6 times weekly, with very heavy weight. If deep squats were so bad for their knees, they wouldn't be able to squat that deep, that often, and that heavy.

Partial squats, however, will NOT activate the hamstrings, and the amount of shearing force on the patellar tendon increases exponentially. What WILL happen if you do partial squats is that your quadriceps will become disproportionately strong as compared to your hamstrings, and the following are likely results:

In partial squats, the hamstrings aren't activated, which means the patellar tendon takes up all the strain/stress/pull during squats. As a result, fatigue and damage to the tendon can accumulate because tendons recover MUCH slower than muscles. Any type of action involving knee bend can then cause further stress and strain during daily activity. This is asking for trouble. If the hamstring is strong, it drastically reduces the amount of stress on the patellar tendon. Full squats make the hamstrings strong. Partial squats allow the hamstrings to become weak. Weak hamstrings are bad Bad BAD.

Partial squats develop the quads and neglect the hamstrings. Weak hamstrings coupled with strong quads result in hamstring pulls while sprinting, starting or stopping suddenly, playing sports, etc.. They frequently occur as the result of muscular imbalances across the knee joint. Strong quadriceps and weaker hamstrings result in a knee joint that is unstable during rapid acceleration and slowing, and the hamstrings are unable to counteract the powerful forces that occur during sudden stops and starts. In other words, you do a sprint with extra-strong quads and weak hammies, and you are begging for a pulled hamstring because your hamstring isn't as strong as the quads and isn't able to perform an adequate eccentric contraction to keep your knee joint from hyperextending during a sprint. As a result, you strain the hamstring because, although it isn't strong enough to do the job, it will hurt itself trying.

In sports, your acceleration will be weak, as will your jumping ability, as a result of underdeveloped hamstrings and hips. Poor speed/acceleration = poor performance

You will end up using stupidly heavy weights in the partial squat due to the mechanical advantage afforded by partial squats, and you put your back and even shoulder girdle at risk due to the extreme loading of the spine."

Listen to your body. Listen to a sports trainer. Half-listen to your PT. He/she may or may not know depending on experience. The group moderator above has good advice. Usually, a Dr knows squat.

My daughter is an Olympic athlete with a couple of golds. She has been through more knee injuries than you can shake a stick at. Even to the point of walking on crutches and not being able to drive. Once i had to move to a national training center and chauffer her around to dr appointments and pt sessions because she couldnt even use that knee enough to drive. She recovered every time with good sports trainers and won her golds after recovery. You can do this. She would tell you to listen to your body but don't give up training.

My knees improved immensely when I lost weight. Lots of things are going to change as you lose weight. Listen to your body as #1.

Before taking that advice from the physical therapist I would try and find a physical therapist that has actually legitimately done squats. Most of them say stuff like that.

Before taking that advice from the physical therapist I would try and find a physical therapist that has actually legitimately done squats. Most of them say stuff like that.

Yes, this was my concern. She made other comments about full squats only being for bodybuilders. I thought it was odd.

That is a load of bullsh!t. I would definitely get another PT, one who has (as suggested by the prior poster) actually done squats ('proper' ones).

That's good. I found a PT for my son who used to play college baseball. He is way more knowledgeable than most of the other PTs that I have spoken with.

Good luck.

Regarding my previous suggestion about finding a PT who actually has done squats, good luck. Most of them haven't and this includes doctors (including orthopedics, chiropractors), and even individuals with grad degrees in kinesiology.

There was a great web article I found about the origins of deep squats being bad for the knees myth. I wish I could find it. Essentially there was only one poorly constructed study that stated this, but everyone has latched on to this notion. Boggles my mind.

You are more likely to have back issues than knee issues from deep squatting. This has to do with the level of hip mobility you have or lack there of. If you lack mobility you will experience butt wink the lower you go down.

I have a PT in mind- he's a family friend and works part time for the local high school working with athletes. He's also in fantastic shape so I assume he'll know more. I just went to the PT my doctor recommended first (a therapy office he's financially invested in...) I'm glad to be switching now.

Thanks for the feedback everyone. It has been helpful.