Line a baking sheet with waxed paper.

Place flour into a shallow bowl. Whisk eggs and water together in a second shallow bowl. Whisk cornmeal, salt, and pepper together in a third shallow bowl.

Dip one tomato slice into flour, then dip into egg mixture. Press tomato into cornmeal mixture, then shake off excess and place onto the prepared baking sheet. Repeat with remaining tomato slices, arranging them in a single layer on the baking sheet.

Heat 1/4 inch canola oil in a large skillet over medium heat until shimmering. Working in batches, fry tomatoes in hot oil until golden and crisp, 3 to 4 minutes per side. Drain on paper towel-lined plates.