Susceptible joints:
Shoulder- swimmers with poor technique (crossing arms midline during the pull, e.g.) can acquire shoulder problems like impingment syndrome, rotator cuff tears, and labral tears. Keeping one's hands/arms in line with the shoulder can prevent these types of problems as well as dry-land strengthening and conditioning aimed at improving muscular endurance.
Knee- meniscus tears are potentially high for the breastroke- that whipping frog kick can wreak havoc on the menisci, which are susceptible to twisting-type injuries.
Back- I've treated a number of swimmers in the past with back problems. Disc herniations, bakc strain and spasms are among the few. In fact, there are some types of back disorders where specific strokes should be avoided. For example- spinal stenosis (which usually occurs in the >50 crowd) sufferers should limit or avoid butterfly, freestyle or breastroke because lumbar extension is what worsens their symptoms in the first place. When I get a patient who tells me that their physician recommend swimming, I'm very careful about what exactly they'll be doing in the pool.
So, while swimming is an awesome calorie burning and cardiovascular activity, it is not as safe as people may think of it to be!