The Santa Clara Valley Water District began studying this watershed with emphasis upon flood control functions, and made some minor streambed alterations such as energy dissipators.

In 1976 the District developed a comprehensive flood control plan and retained Earth Metrics Inc. to prepare an independent Environmental Impact Report.

[6] The resulting study developed the first comprehensive data base of biology, water quality, geology and cultural resources information for Alamitos Creek.

In 1989 the city of San Jose undertook an analysis to create a creekside trail from Almaden Quicksilver County Park to a location along Alamitos Creek about .6 mile below the confluence with Arroyo Calero.

“Rainbow trout in Barret Creek were [once] so plentiful that fishermen used to catch them by the hundreds,” said Vice President Marti Tedesco of the Peninsula Open Space Trust.

Lake Almaden is a great impediment to native steelhead trout (Oncorhynchus mykiss) migration, as it is home to many non-native predatory fish, such as largemouth bass (Micropterus salmoides).

It also serves as a heat sink elevating river water temperatures downstream and creating a large warm lake area difficult for trout to migrate through.

The California Office of Environmental Health Hazard Assessment has issued a "Do Not Eat" for any fish caught in Alamitos Creek due to elevated mercury.