The main reasons why your homemade Tzatziki Sauce may become watery is if you didn’t properly strain your cucumbers after grating, or if you should have used strained yogurt. Be sure to let the grated cucumber sit for a few minutes and then squeeze out the excess moisture before adding to the rest of the ingredients. As for the yogurt, if your Greek yogurt is on the thinner side, strain it through cheesecloth to remove some of the moisture.