Temporary streams in California and other Mediterranean climate areas are among the aquatic habitats most altered by human actions and by invasions by alien species. They typically support novel ecosystems, defined as ecosystems dominated by new combinations of organisms in highly altered habitats. Although these new ecosystems have many attributes of the ecosystems they replaced, such as native species, they typically contain many new interactions among species. Managers need to recognize this reality to find ways to direct change towards novel ecosystems with desirable features, including native species. The concept of reconciliation ecology is a practical approach to living with the new reality; it includes actively guiding ecosystem change, as illustrated by Putah Creek, Cosumnes River, Eel River and Six Bit Gulch in California. The first three waterways are all highly altered and managed with varying degrees of success to favour desired aquatic species, whereas Six Bit Gulch experiences such extreme conditions that the original ecosystem is still largely intact. The examples illustrate that most aquatic ecosystems in California are so highly altered that attempting to restore them to an earlier condition or stable state is largely not possible. Where more or less intact systems persist, it is usually because extreme environmental conditions restrict both alien invaders and human use in small watersheds. This pattern appears to be fairly typical of streams in Mediterranean climate areas.