Data from: Multitrophic responses to tidal marsh restoration: Early effects of channel configuration on water quality, aquatic food web structure, and fish communities

Introduction: Tidal wetland restoration is critical for reversing habitat
loss and enhancing estuarine resilience under accelerating sea‑level rise
and climate variability. Dutch Slough in the San Francisco Estuary served
as a living laboratory for adaptive management and ecosystem recovery.
Objectives: We assessed early ecological outcomes of a tidal wetland
restoration design, focusing on how channel length, complexity,
connectivity influence functional recovery and habitat quality across
variable climate. Methods: Two constructed tidal channels and one large
open-water feature were monitored from 2021 to 2023 using a
Before–After–Reference–Impact (BA:RI) framework. Mixed-effects BA:RI
models isolated restoration effects. Data collection integrated continuous
water-quality sensors, machine-learning-based zooplankton imaging, and
video sampling and environmental DNA (eDNA) for fish.  Here, we
evaluate aquatic food‑web responses using coordinated indicators spanning
primary producer biomass, zooplankton assemblages, and fish abundance and
composition during early restoration. Results: Pre‑breach (2021): Three
isolated aquatic food webs formed, and water quality differed
significantly from reference sites. Post-breach (2022–23): Conditions
shifted toward reference states, with improved dissolved oxygen, dynamic
turbidity, and reduced chlorophyll-a linked to shorter residence times and
enhanced tidal mixing. Despite lower chlorophyll-a concentrations,
observed patterns were consistent with our expectation of altered
production pathways characterized by rapid turnover rather than reduced
production, suggesting a shift from biomass accumulation toward rapid
export and trophic transfer rather than diminished productivity. Longer,
more complex channels supported greater habitat heterogeneity, higher
zooplankton and juvenile fish densities, especially near vegetated
margins, and increased species richness. eDNA and video surveys detected
rapid fish taxa increases post-breach, including seasonal expansion of
native taxa amid persistent non-native dominance. Conclusions: Channel
length, complexity, and connectivity strongly influence ecological
rehabilitation. Adaptive management accelerates functional restoration and
improves nursery habitat quality. Implications for Practice: Restoration
designs should prioritize structural complexity, dendritic channels, and
vegetated margins to enhance food web support and fish recruitment.
Connectivity reduces residence time and drives measurable shifts in
water‑quality conditions toward reference states (e.g., dissolved oxygen,
turbidity variability, salinity gradients, and chlorophyll‑a), while
potentially enhancing nutrient exchange. These strategies increase
ecological return on investment by fostering biodiversity and resilience
in subsided, highly invaded landscapes. Adaptive management (integrating
monitoring with iterative design refinements) remains essential for
sustaining benefits under climate change. Practitioners should pair
physical complexity with long-term data collection to ensure restored
wetlands deliver ecosystem services such as carbon sequestration, flood
protection, and fisheries support.