Although Kyoto receives a lot of rain showers and humidity during early summer, it is also a great time to witness lovely water lilies all around beautiful Japanese gardens and waterparks.
The Heian Jingu Shrine is one of the most well-known places to spot water lilies in Kyoto, due to its marvellous gardens. It was built in the style of the Heian Period with a classic Japanese wooden bridge named Taihei-kaku. There are many ponds where you can view the gorgeous water-loving flowers, irises and other greenery.
Another eye-catching place is the Kajū-ji Buddhist temple, where you can find the Hyōchi-en garden with great ponds and picturesque panoramas. It's home to a variety of pink and white lilies, lotuses and water birds. Also, Hiei Garden Museum is a good spot for waterlilies. And if you don't mind travelling a bit out of the city, you can visit Hatada pond in Nozasa known as "suiren ike", that's literally "water lily pond".
The best time to enjoy these water flowers is from mid-May to mid-September. Keep in mind that water lilies close their buds in the afternoon, so it's better to go to see them early in the morning.