Which beach has the calmest water for small kids?
The bay side, not the ocean side. Mission Bay is a sheltered aquatic park protected from Pacific swell — that distinction matters far more for small kids than which beach town you pick.
Most named "beaches" here front the open Pacific, with real shorebreak. Mission Bay is a different body of water: a large protected aquatic park separated from the ocean, so it has no meaningful surf.
For toddlers and non-swimmers, that is the whole ballgame. Bayside spots like Bonita Cove, Ventura Cove and Fiesta Island have shallow, flat water and gradual entry. Two hundred yards away on the ocean side of the same peninsula, Mission Beach has waves that will knock a five-year-old over.
So the useful question isn't "which beach town" — it's "bay or ocean." A family can stay in Mission Beach or Pacific Beach and simply walk to the bay side for the calm-water day.
One caveat worth knowing: after heavy rain, county advisories often recommend staying out of the water for 72 hours near storm-drain outlets, and enclosed bay water flushes more slowly than open coast. Check current advisories before a bay day in winter.