Perhaps compare squats to push-ups or running to boxing. If you are used to doing exercises involving primarily the lower body, squats or running for 30 min probably seems much easier than doing 30 min of push-ups or continuous sparring/heavy bag work. Yet, both squats and running will burn more calories for a given amount of time for the reason George mentioned.
Also, the intensity involved in swimming may seem much higher to you now than running because I gather from your other posts that you are still learning to become an efficient swimmer. And in fact, you may actually be burning more calories than an efficient swimmer of the same physical build swimming at the same rate.
Lastly, water tends to cool the body and keep one's heart rate lower when working out than while exercising in air. So generally you'll need to workout more intensely to keep your heart rate elevated in water than on dry land. At least, that's what my books on doing water-based aerobics tell me.
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