I'm looking for lot planning suggestions

I have attached a topo for our 5 acre lot in Northern California. We are currently planning a passiv house + earthworks to be started next year and I am looking for suggestions on overall layout. I want this layout to exist long term and want to get it right.
We are zone 9a, average 30 inches of rain between Nov-April, dry the rest of the year. Sandy loam soil. I'm hoping to capture and recharge water above the planned gardens in addition to some storage. I need to account for a leach field.
North is to the left. There is an existing small house and garage on the NE corner that we want to turn into a grannie unit. The new house is near the rainwater storage tanks. Our civil engineer wants to put the leach field just to the south of the house - that takes valuable zone 1 space. I want to push it further south and put in a water recharge pond with gardens below. Between the existing house and secondary recharge pond is an existing dry farmed apple orchard that we are resuscitating from long neglect.
There is a spring fed year round creek at the southern border of the property. The southern ~1/4 of the property is re-wilding zone 5 area.

Our goal is to create a regenerative permaculture homestead.

Does anyone have experience with water recharge ponds like this? Will they be an asset or a nuisance (algae, smell, problems when dry)? Is it possible to contain water like this when there is a high gopher population?

Thank you in advance for reading all of this and creating thoughtful replies.