What is the life-cycle of agricultural water used to grow crops/animals?
The water cycle isn't geology, but it's important to pedology, which is an earth science. 

Agricultural water can be converted (by photosynthesis) directly into simple carbohydrates that we eat; or converted into carbs and then used as structure or energy that keeps the organism alive and growing, but isn't the mass we finally eat; or used to build more complicated parts of the organism (fats, protein) that we finally eat; or transferred to the atmosphere (mostly) because none of these biological processes are leak-proof; or transferred to the atmosphere or groundwater because we don't get all the water to the plant roots exactly when the plants can use it. 

If we eat meat, there's all of the above in making the plants the animal eats, and then even greater inefficiency in turning water-in-plants into animal flesh, and the greater structure and energy costs to keep the animal alive and growing. 

The crops listed are not simple carbs, or even self-fertilizing legumes. It takes a lot of tree to make an almond or an avocado. It takes a lot of water to grow the alfalfa and grains that we fatten cows on. There's also water in the processing, the cold chain, often in generating the power that makes nitrogen fertilizer or moves food from California (CA) to the markets.  CA's main ag land is dry and warm and often windy in the summer, so it can lose water really quickly (either through the plants or from flood or overhead irrigation, and even a little bit through mulched soil). 

I don't know about all of CA (it's a big place with a lot of different climates), but at least some -- the west side of the Central Valley -- is having soil trouble because they rarely get enough irrigation or rain to flush salts and excess fertilizer out of the root zone, so they at least aren't sending excess water to groundwater. One could check stream gauges to guess whether excess water is making it into surface water -- my guess, not.