The San Juan River splits into several tributaries that drain into Port San Juan. The reserve is divided into two sections, one lies along the north bank of the north segment of the San Juan River, while the other is in the flood plains to the southwest, along the most south segment of the San Juan River. The southern segment of the reserve is the larger of the two and has six tributaries. The small north section flows into the Gordan River Estuary, the southern section is the main river and it flows into Harris Cove, just above the bridge the cross at the outer edge of Port Renfrew. Harris Cove is a great place to go birding and just at the bridge, you can enter a great campground on San Juan Beach.
The cover growth is made up of small sections of coniferous trees along with a large deciduous forest of alder, cottonwood, and maple. Some species of plants here are quite rare, they include the angled bitter-cress, smith’s fairy bells, tooth-leaved monkey-flower, paintbrush owl clover, nodding semaphore-grass and pink fawn lilies, salmonberry, piggy-back plant, red alder, currant, and lady fern.
The wildlife here in the San Juan River Estuary is incredible, you have a great chance of seeing black bears, deer, cougar, martins or raccoons along of numerous birds of all types. Looking out to sea, you could see gray whales, sea lions, and seals.
Kayakers love the area as there is so much to this huge estuary that you could kayak here for a week and still not see it all, there is a great campsite at the northern end of the estuary that is on the Pacheedaht Reserve and is right on the Pacheedaht Beach, this is one of the nicest campsites in the area.