Early indicators of tidal ecosystem shifts in estuaries

Tidal ecosystems provide disproportionate ecosystem services (flood risk mitigation, carbon sequestration, fish nursery functions) but are being altered by global change (e.g., sea-level rise) and regional anthropogenic activities (e.g., channel deepening, land reclamation) that modify hydrodynamics and geomorphology. Many estuaries have been deepened and narrowed to support shipping, amplifying tides and currents while altering wave climates, which biases sedimentation and transforms gently sloping tidal flats into systems with sharp transitions between high intertidal flats and deep channels. Ecologically, transitions from bare flats to vegetated marshes affect services and biodiversity, creating management trade-offs. These transitions can be rapid once triggered due to reinforcing feedbacks and are often framed as shifts between alternative stable states. Therefore, early indicators that precede the onset of ecological transitions are needed. This study asks whether the emergence of micro-topographic patterns on tidal flats serves as an early indicator of impending marsh establishment, and investigates the environmental conditions under which such patterns form, using large-scale geospatial datasets from three European estuaries and a simple numerical model.

Prior work links marsh establishment to tidal elevation and inundation dynamics, particularly the need for periodic refuge from inundation (windows-of-opportunity) allowing pioneer seedlings to survive hydrodynamic stress. Predictive studies typically use elevation and local hydrodynamic forces to forecast vegetation presence. Small-scale studies suggest micro-topography (meter-scale ridges and runnels with up to ~10 cm relief) enhances subsurface drainage and oxygenation, reduces sulfide toxicity, and can facilitate pioneer establishment and reduce erodibility. However, most evidence comes from de-embanked restoration sites or experiments with artificially created micro-topography, leaving gaps about natural formation conditions, prevalence in estuaries, and their role in large-scale vegetation expansion. The framework of alternative stable states explains rapid ecological transitions, but early-stage geomorphic precursors have been underexplored at decadal and estuary scales.

Study design combined: (1) geospatial analysis of publicly available aerial lidar elevation data, false-color orthophotos, and tide-gauge time series for three European estuaries (Dutch Western Scheldt, British Humber, German Elbe); and (2) a simple numerical model of shallow surface-water drainage over inclined planes with small-scale roughness.

Data sources and preprocessing:

• Western Scheldt: Annual lidar (2–5 m horizontal, ~1 cm vertical resolution, 2004–2020) and orthophotos (NIR, red, green bands, 12.5–25 cm, 2004–2020 semi-annual subset). Water levels from 5 stations (2004–2020) to convert elevation to frequency of skipped inundations; longitudinal interpolation between stations.
• Elbe: Lidar (1 m horizontal, 1 cm vertical, 2006, 2010, 2016), orthophotos (25 cm, 2006, 2010, 2016), and biotope/vegetation polygon maps (2002, 2006, 2010, 2016) rasterized to 10 m for vegetation presence. Water levels from 10 stations along-estuary, interpolated longitudinally.
• Humber: Lidar (1 m, 1 cm, 2001–2019 diverse years), orthophotos (20 cm, 2011–2018). Water levels available only at Immingham; analyses constrained spatially near that station. Some year misalignments addressed by pairing near-contemporaneous datasets (e.g., 2010 lidar with 2011 imagery). All analyses resampled to 10 m to match micro-topography metric.

Tidal inundation metric:

• For each estuary and year, computed the percent of skipped tidal inundations at each intertidal elevation: 100% × [1 − (number of high tides exceeding elevation)/(total tidal cycles during the record)]. When multiple stations existed, calculated per station and interpolated between stations to account for along-estuary tidal amplification.

Vegetation mapping:

• Calculated NDVI from orthophotos (red, NIR). Year-specific NDVI thresholds set using bimodal peak analysis (sediment vs vegetation peaks) and threshold halfway between peaks. In Elbe, official biotope polygons were used in place of NDVI. Rare misclassification from epibenthic algae (e.g., Vaucheria) acknowledged but considered minor for conclusions.

Micro-topography detection and calibration:

• Defined intensity of micro-topography as the standard deviation of the NIR band within 10 × 10 m windows computed from high-resolution orthophotos, serving as a proxy for ridge–runnel texture. Calibrated this image-based metric against terrestrial lidar-derived slope variability (25 cm grids) at three Western Scheldt sites (2020–2022), finding a strong log–log linear relationship (R² = 0.72, p < 0.001), supporting reliability when bathymetric lidar resolution is insufficient to resolve cm-scale relief.
• Excluded confounders: masked vegetated pixels (NDVI), areas below neap high water level (to exclude mega-ripples), and tidal creeks identified by local slope >3 degrees (creeks detected at 2 m resolution then expanded and resampled to 10 m to also exclude adjacent banks).

Geospatial analyses:

• Morphological trends: Linear regressions of mean elevation and mean percent skipped inundations over time for upper intertidal flats (above neap high water level). Constructed hypsometric curves of inundation skipping and of slope vs tidal position, to assess rising and flattening trends.
• Vegetation establishment probability: Identified new vegetation between consecutive observation years (1–3 year intervals) where vegetation appeared in the later but not earlier year. Binned all intertidal pixels by two covariates—micro-topography intensity and percent skipped inundations—into a 2D grid (85 × 101 bins). Computed establishment probability per bin as the proportion of pixels that became vegetated in that interval. Averaged across all year-pairs and estuaries to produce a combined surface relating establishment probability to elevation and micro-topography intensity.
• Micro-topography controls: Assessed relationship between pattern intensity and tidal-flat slope by binning slope logarithmically (120 bins) and computing mean intensity per bin. Also related intensity to percent skipped inundations (log–log regression). Analyses conducted in R.

Numerical model of shallow surface-water drainage:

• Constructed a 2D inclined plane (512 × 512 grid) with periodic boundaries and superimposed autocorrelated surface roughness (standard deviation ~2.5 cm at 1 m² cell). Simulated drainage of a thin, initially uniform water layer (depth set to 10% of the roughness SD) under gravity, where local flow direction and velocity depend on the combined gradient of the water surface and underlying plane. Used a simplified flow formulation conserving mass and momentum with constant hydraulic conductivity for very shallow flows. Ran ensembles (n=100) across plane inclinations from 0 to 1.5 degrees, recording time-averaged water height per cell after near-steady drainage. Defined an intensity of flow concentration as the standard deviation of time-averaged water height across the domain, quantifying pooling and channelization. Compared concentration intensity across slopes to observed distributions of micro-topography with slope in geospatial data. Code archived and publicly available.

• Upper intertidal flats above neap high water level rose in elevation and experienced more frequent skipped tidal inundations over the study periods, indicating progressive accretion: Humber (2001–2019): increase in skipped inundations 1.32 ± 0.08% yr−1 and independent elevation trend 1.23 ± 0.21 cm yr−1; Western Scheldt (2004–2020): 0.32 ± 0.02% yr−1 and 1.44 ± 0.10 cm yr−1; Elbe (2006–2016): 0.15 ± 0.001% yr−1 and 1.44 ± 0.00 cm yr−1. Hypsometric analyses showed that flats are flatter at higher tidal positions, consistent across estuaries.
• Vegetation expanded substantially at the estuary scale. In the Western Scheldt, vegetated area increased by 607 ha between 2004 and 2020 (38 ± 6 ha yr−1), with similar net gains in the Humber and Elbe. The fraction of upper intertidal flats that are vegetated in the Western Scheldt rose from 22.5% to 29% over 16 years.
• Probability of new vegetation establishment increases with higher tidal position (more skipped inundations), and micro-topography significantly boosts establishment likelihood, enabling establishment closer to the lower tidal limit (near the neap high water boundary) than in smoother areas.
• Micro-topographic patterns occur predominantly on very gently sloping upper intertidal flats, with intensity peaking near ~0.1 degrees and rarely occurring where slope exceeds ~0.3 degrees. Pattern intensity also increases with more frequent exposure (higher percent of skipped inundations).
• Numerical simulations show that at very low underlying slopes, small-scale bed irregularities cause pooling and linked drainage pathways that concentrate surface flow; as incline increases, flow becomes more sheet-like and less sensitive to small irregularities. The modeled dependence of flow concentration on slope aligns with observed concentration of micro-topography at low slopes, offering a mechanistic explanation for the absence of patterns on steeper flats. The model does not capture the observed drop in pattern intensity at near-zero slopes.
• Proposed early indicator: accreting upper intertidal flats that flatten toward slopes generally below ~0.3 degrees tend to develop micro-topographic patterns, which precede and facilitate marsh establishment across estuaries subjected to anthropogenic deepening and narrowing.

The study dissects the bare-to-vegetated transition into sequential, process-driven stages detectable on decadal and estuary scales: (i) net accretion raises and flattens upper intertidal flats; (ii) low-slope conditions stabilize and intensify micro-topographic patterning; (iii) these patterns facilitate pioneer vegetation establishment through enhanced drainage, sediment oxygenation, and reduced erosion. This stage-based understanding yields a practical early warning indicator—the emergence of micro-topography on flats with slopes typically below ~0.3 degrees—well before rapid ecological transitions commence. Anthropogenic channel deepening and estuary narrowing likely underlie the ubiquity of accretion and flattening by amplifying tides and concentrating sediment deposition near channels, producing convex profiles and expanding high, low-slope flats with reduced wave energy. The inclined-plane drainage model supports a mechanistic link between low slopes and the formation of pooling and preferential drainage pathways, explaining the spatial association of micro-topography and gentle slopes. Increased exposure during high tides likely promotes pattern amplification via drying and reduced sediment turnover. Management relevance is high: early detection of micro-topography on accreting, gently sloping flats can warn of impending marsh expansion, informing trade-off decisions where losses of tidal-flat habitat conflict with gains in marsh services (coastal protection, carbon). While options like relocating ports or managed realignment can mitigate dredging impacts, they entail significant socio-economic costs. The proposed indicator enables proactive, adaptive management within existing constraints.

This work identifies micro-topographic pattern development on gently sloped, accreting upper intertidal flats as a robust, estuary-scale early indicator of transitions from bare tidal flats to vegetated marshes. Combining multi-year, multi-estuary geospatial analyses with a simple drainage model, the study shows that micro-topography typically emerges where slopes are below ~0.3 degrees and precedes vegetation establishment by enhancing biophysical conditions for pioneers. The indicator generalizes across three European estuaries subjected to deepening and narrowing, suggesting broader applicability under similar morphological management regimes. Future research should (1) establish causal mechanisms of pattern initiation and maintenance, especially at near-zero slopes; (2) integrate hydrodynamic, sedimentological, and biogeochemical drivers with biotic precursors (e.g., biofilms); (3) validate thresholds and timelines with targeted field experiments and higher-frequency monitoring (e.g., UAVs); and (4) assess transferability to other tidal regimes and anthropogenic contexts to refine early-warning frameworks for biogeomorphic transitions.

• Evidence is primarily correlative at estuary scale; causal mechanisms of micro-topography formation remain incompletely resolved.
• The simple inclined-plane model does not reproduce reduced pattern intensity at near-zero slopes and omits full tidal cycles and sediment transport/erosion mechanics.
• Remote sensing constraints: lidar vertical/horizontal resolution can miss cm-scale relief; orthophoto-based micro-topography metric may confound with other textured features despite masking efforts.
• Vegetation mapping via NDVI can misclassify epibenthic algae (e.g., Vaucheria) as vegetation; year-specific thresholds introduce variability.
• Tide-gauge coverage limitations (e.g., single station in the Humber) required spatial restriction and interpolation assumptions elsewhere.
• Temporal coverage varies among estuaries (shorter records in the Elbe), potentially affecting trend robustness.
• Masking thresholds (e.g., slope >3 degrees for creeks, above neap high water for micro-topography focus) may exclude edge cases or introduce classification biases.