If you are looking to combine history and nature, save a half day in your San Diego travel plan to visit the Cabrillo National Monument. Operated by the National Park Service, the monument commemorates the landing of Juan Rodriguez Cabrillo at San Diego Bay on September 28, 1542.
Not far from the visitor center and parking lot, you will find the Old Point Loma Lighthouse and Cabrillo statue overlooking the harbor and ocean. To keep focused on the history and nature, I've written a separate article about the lighthouse. Standing at 422 feet above water views, you'll want your camera to capture
the breathtaking views. If you visit during whale migration season (December through March), use your id to borrow binoculars from the visitor center. You might see 30 to 50 foot long gray whales. Peak time to see the whales is mid-January.
If I could repeat the visit, I would have allocated more time. I visited in February and it would have been the right time to see the tidepools. Late fall and winter are the best times to visit the tidepools. It's only a one mile hike. Go two hours before low tide times. Check the NPS website for tide charts. The depressions in the rocks along the coastline capture animals during low tide (when water recedes) which would create a great nature exploration for kids. Make sure they wear shoes that won't easily slip on the wet rocks.
If I could choose anytime to visit, I would time the visit to the Cabrillo Festival in September. It's a free festival with cultural music and dancing, food from Mexico, Portugal, and Spain, and Kumeyaay baskets and other crafts. I'd time arrive in time for the 1PM re-enactment of Cabrillo's landing on Ballast Point. If you want to help support, buy tickets (approximately $30) for the evening social reception.
The National Park Service brings history alive. If you are interested in another way to teach your kids through travel about early Spanish explorers, visit my article on the DeSoto National Memorial.