Abstract1. Intermittent streams are hydrologically dynamic within and among years, leading to episodic bouts of local extirpations and subsequent recolonisation of vertebrate groups such as fish and larval amphibians. As these aquatic habitats undergo drying and enter states of incomplete recovery, their ecosystem functionality is impacted. We investigated the legacy effects of drying and refilling of wetlands via mesocosms on growth and survival of recolonising aquatic vertebrates and their subsequent effects on ecological function. Specifically, we tested the effects of prior drying on anuran and fish growth and survival (using Gompertz growth curves), the joint effects of vertebrates and drying on periphyton biomass, and whole‐system gross primary productivity.2. Using 64 1000‐L hard plastic cattle tanks to create replicate aquatic mesocosms, four trophic treatments (no vertebrate control, larval anurans, fish, larval anurans and fish) were crossed with two drying treatments (undried and dried–refilled) to simulate different outcomes of colonisation by two common vertebrate guilds and drying/refilling cycles. Mesocosms with anuran treatments received 50 Lithobates blairi tadpoles (1600 total) and mesocosms with fish treatments received one Lepomis cyanellus juvenile (32 total). We recorded anuran growth rates, survival and time/size at metamorphosis, fish growth, gross primary productivit, and periphyton biomass over 12 weeks from 9 May 2021 to 1 August 2021.3. Prior drying strongly reduced L. blairi growth rate by 38.2% but increased survival from 48.5 to 75%, resulting in relatively equal emergent anuran biomass between the two drying treatments. No L. blairi survived to metamorphosis when co‐occurring with fish (i.e., larval anurans and fish treatment). On average, prior drying reduced the size at metamorphosis by 35.5%, delayed time to metamorphosis by 4 days, and increased the range of metamorphosis days by 10 days. Fish growth and survival were unaffected by trophic or drying treatments. Gross primary production and periphyton biomass decreased in response to prior drying and the presence of larval anurans, but these effects were non‐constant over time.4. The effects of short‐term drying were not immediately reversed by refilling and were still perceivable across nearly all trophic levels several months post‐refill. However, for generalist colonisers such as L. cyanellus, optimal habitat is minimally impacted by drying history of the aquatic habitat and depends primarily on the presence of water and connection to source populations. Colonisation by fish removed an entire consumer guild (anuran larvae) and an aquatic–terrestrial flow of resources (anuran juveniles).5. Climate change is increasing the frequency and severity of droughts and drying events around the world, and increasingly leaving ecosystems in an incomplete state of recovery. Intermittent streams are particularly well‐suited for studying dry–refill cycles as they are one of the most common global freshwater systems. While several studies have investigated the contemporary effects of drying on aquatic systems (i.e., what happens to organisms when a pool dries), this study addresses gaps in our understanding of legacy effects of prior drying on aquatic organisms and ecosystem processes after water returns. Here we clearly show that even short‐term drying has pervasive effects on aquatic ecosystem function following refill.