This is the most important difference between the two, and it goes both ways.
Rethymno has the beach in town. A sandy beach runs east from the edge of the old town for about 12 km, with sunbeds, lifeguards in season and water that gets deeper gradually. You can be in the sea five minutes after breakfast. It's an open north-facing beach, though, and on windy days red flags go up for good reason: in August 2026 lifeguards made ten rescues in 45 minutes there, all of people who ignored the flags. In summer the meltemi, the strong northerly wind of the Aegean, can blow for days and makes both towns' north-coast beaches rough.
Chania has the famous beaches. The town beaches are fine but small: Nea Chora is a 1 km walk west of the old town, and the better sand at Chrysi Akti and the little coves of Agioi Apostoloi is 2.5-5 km west, with city buses every 20 minutes. The real reason to stay in Chania is the beaches within a day trip. Stavros and the narrow inlet of Seitan Limania on the Akrotiri peninsula are half an hour away, Falassarna about an hour, and the Balos lagoon and the pink-tinged sand of Elafonisi one and a half to two hours. Balos means an 8 km dirt road and a hot 20-30 minute walk each way, or the boat from Kissamos, and Elafonisi has one bus a day. From Rethymno, each of these is roughly an extra hour each way.
Rethymno's answer is the south coast: Plakias, Damnoni and the palm grove at Preveli, where a river meets the Libyan Sea, are 45-50 minutes away, and Triopetra and Agios Pavlos about an hour. The sea there is often flatter when the north wind blows, though gusts can be strong (Plakias is known for them). Preveli has only two buses a day from Rethymno, and the beach is a steep 10-15 minute walk down from the car park. From Chania, these beaches are a two-hour drive.