Long-term data are needed to assess spatial and temporal variability of communities and their resilience to natural and anthropogenic disturbances, particularly in climatic regions marked by high interannual variability (e.g. mediterranean-climate). A long-term study at four sites on two streams in mediterranean-climate California (annual sampling over 20 yr) allowed us to quantify the influence of a 5-yr prolonged drought on stream invertebrate and fish communities. Invertebrate community composition did not show recovery following drought. The primary environmental factors influencing community composition, identified through principle components and multiple correspondence analyses were precipitation and flow permanence. Invertebrate taxon richness and abundance exhibited few responses (some site specific) and recovered quickly. Native fish abundance was lowest during the drought period and highest during the wet years that occurred at the end of the study period. Importantly, the prolonged drought facilitated the establishment and success of the invasive green sunfish (Centrarchidae: Lepomis cyanellus) that was then resilient to subsequent large flow events. There was high spatial synchrony in the temporal changes among all four sites, and three distinct periods were identified: early drought, late drought, and post-drought years. However, we still found differences among sites along the flow permanence gradient from temporary to perennial in the response to drought of both invertebrate and fish assemblages likely as a result of changes in substrate, vegetation, and other habitat characteristics. The observed lack of resilience and negative impacts to biodiversity due to prolonged drought associated with long-term habitat changes is important because hydroclimatic extremes are predicted to increase in frequency and magnitude with global climate change.