Hypertrophy means an increase in the size of a muscle.
The best way to lose fat and improving tone is to do interval training. You will build some muscle but you will not look like the Incredible Hulk. The muscle you build will improve the appearance of your body especially if you lose fat.
In interval training, instead of long swimming (or running or bicycling), an exerciser/athlete does shorter distances on a certain time interval.
For example, instead of swimming (in a high school pool) a 1000 yards straight, the swimmer swims twenty 50 yard swims starting a new swim every (for example) minute. A shorthand style of writing is used for the intervals and is as follows: S 20 x 50/1. So, if you do one 50 yard swim in 40 seconds, you'd get 20 seconds rest and then start the next swim.
To do intervals, you need a stopwatch (like a water resistant wristwatch) or a pace clock like swim teams use (about 30" in diameter). When someone does intervals, they normally put more effort into a series of short swims than into one long swim. As a result, the swimmer keeps a more elevated heart rate, waste products are produced that stimulate your body to get into better shape, and by going faster there is more resistance which makes you stronger.
In addition, doing intervals allows for a huge variety in your swims. Here are several ways you could swim, or kick, or pull a 1000:
1. S 20 x 50/1
2. S 10 x 100/2 or 2:30
3. S 1 x 400/7
S 1 x 300/5:30
S 1 x 200/4
S 1/ 100/2
So, there are basically four variables that you can manipulate in planning what you are going to do
1. Swim, kick, pull as well as which stroke or IM
2. How many repetitions
3. How far is each repetition
4. the time interval.
Your thighs, based on your description, are mostly muscle. If you want to 'lean' them out more, you should do long distance training. If you want to KICK on a kickboard in the pool, then consider kicking 5 x 200/5 minutes ... or going out and jogging 4-5 miles.
Keep in mind that there is no such thing as spot reduction of fat. Fat comes off your body pretty much uniformly. Some areas might have more or less to lose but, that is all.