Learn Dutch: Het water in het meer is schoner dan in de rivier. - The water in the lake is cleaner than in the river.

This is because of the Dutch spelling rules for long vowels. When you add the -er ending to schoon, the word splits into syllables like this: scho - ner. Because the first syllable now ends in a vowel (an "open syllable"), a single 'o' is enough to keep the long "oh" sound. Writing schooner would be incorrect.

We use dan for "than" here. Can I use als instead?

In standard Dutch, you must use dan when making an unequal comparison (when one thing is more or less than another). You only use als for equal comparisons, like even schoon als (as clean as). You might occasionally hear native speakers use als instead of dan in casual speech, but it is considered a grammar mistake.

Doesn't schoon mean "beautiful", similar to the German word schön?

In standard Dutch, schoon almost always means "clean". If you want to say "beautiful", you should use mooi or prachtig. However, if you travel to the Flemish-speaking parts of Belgium, you will hear people use schoon to mean "beautiful"!

Do I have to repeat the word in after dan?