There was a ton of guessing involved. One of the key guesses, which turned out to be correct, was that all the metals were elements. But people also guessed that "earths" were elements -- we now know they're oxides of the true elements.

Lavoisier made an influential list of elements, and some of them were wrong. He listed lime, magnesia, alumina, baryte, and silica as "earth" elements. He also missed some, like sodium, even though derived substances like lye and salt were well-known.

Lavoisier also guessed, based on analogies with known elements, that there were some elements that had not yet been isolated, like fluorine and chlorine. Interestingly, his reasoning was wrong. He thought that acids were produced by a nonmetal reacting with oxygen. Therefore, the existence of "muriatic acid" meant that there must be some "muriatic" element which combined with oxygen to produce this acid. In reality, muriatic acid did contain an unknown element (chlorine), but oxygen wasn't involved -- it's just HCl.

Most of Lavoisier's mistakes were resolved fairly soon. Davy isolated calcium, barium, and magnesium, which was fairly convincing evidence that the other "earths" were really compounds of unknown metals. (He also made chlorine, sodium, and potassium.)