About

Stephen Monismith is the Obayashi Professor in the School of Engineering and a Professor of Oceans at Stanford University. His role involves research and teaching in the field of civil and environmental engineering, with a specific focus on ocean-related studies. As a senior faculty member, he contributes to advancing knowledge in his area of expertise, although the specific details of his research focus and key contributions are not provided in the page text.

Research topics

• Biology
• Ecology
• Physics
• Oceanography
• Geology
• Environmental science
• Environmental health
• Mechanics

Selected publications

• Salinity simulations in San Francisco Bay

  2026-02-12

  book-chapterSenior author

  A three-dimensional hydrodynamic and scalar transport model is applied to simulate salinity in South San Francisco Bay. All model parameters are identical to those used in a model CaUbration in which the model was shown to reproduce current meter data accurately. The 64 day time period studied is characterized by low freshwater input. For this period the salinity data is reproduced well by the model. Because no model parameters are adjusted, the saUnity simulation is considered to be a Validation of the model. The Validated model is used to investigate the effect of wind forcing on the model results.

  PublisherDOI

• Measuring Metabolic Fluxes on Shallow, Wavy Coral Reefs

  Journal of Geophysical Research Oceans · 2026-01-30

  articleOpen accessSenior author

  Abstract In‐situ, metabolic flux measurements are increasingly being employed in shallow coastal settings to monitor ecosystem health, quantify carbon sequestration and understand biogeochemical cycling more broadly. However, the effectiveness of these techniques in wavy environments with high‐relief roughness remains unclear, as waves and canopy dynamics may modify turbulent mixing. We present measurements of net community production (benthic oxygen flux) from three sites along a wave‐exposed fore reef in Palau, using three different approaches: (a) aquatic eddy covariance, (b) scalar variance, and (c) gradient flux. Results are compared between methods and evaluated across a wide range of mean flow and wave conditions. Eddy covariance measurements were separated into wave‐ and turbulence‐induced fluxes using the Benilov method, a spectral technique commonly used to correct wave bias in momentum flux measurements. Removing wave fluxes from eddy covariance measurements improved agreement between NCP rates at the different sites, suggesting that waves primarily contributed to measurement bias and not to real fluxes for our data sets. With this bias removed, NCP measurements were well correlated across the three methods, even when waves were large relative to mean flows. The primary difficulty in implementing scalar variance and gradient flux methods was identifying the appropriate mixing‐length to parametrize eddy diffusivity. While should be equivalent to the measurement height above the coral substrate, this distance is hard to constrain in environments with nonuniform, canopy‐like roughness such as coral reefs. We discuss challenges and provide recommendations for metabolic flux deployments in shallow coastal environments with waves.

  PublisherOA PDFDOI

• Wave transformation over periodic spur and groove bathymetry on coral reefs

  SSRN Electronic Journal · 2026-01-01

  preprintOpen accessSenior author
  PublisherDOI

• Morphologically driven sedimentation patterns on a coral reef

  Coral Reefs · 2025-02-17 · 2 citations

  articleOpen access
  PublisherOA PDFDOI

• In-situ Measurements of Giant Kelp (M. pyrifera) Motion

  2025-10-28

  preprintOpen accessSenior author

  Kelp forests are an important coastal ecosystem, supporting nearshore fisheries, carbon sequestration, and ocean acidification mitigation. Giant kelp (Macrocystis pyrifera), common in temperate environments, are buoyant, flexible, and surface-canopy forming. The three-dimensionally complex structure of giant kelp modifies local hydrodynamics via drag and wave dissipation. Their high flexibility and dynamic motion causes time-varying drag generation, but the underlying mechanisms remain poorly understood. To quantify how giant kelp alters flow, we must first understand how they move in response to varying tidal, current and wave conditions. In this study, we used pressure sensors and 9-axis inertial measurement units to measure the motion of two giant kelp plants under combined forcing from tides, currents, and waves. Our findings reveal that strong currents can induce significant tilts– up to 57 degrees from vertical positioning– over longer timescales (greater than 5 minutes). On shorter wave-driven timescales (less than 30 seconds), motion is amplified near the seafloor. Wave motion can also enhance the average tilt response of kelp to currents. Additionally, removing the surface canopy increases kelp motion near the surface across both shorter and longer timescales, although this effect attenuates with depth. Our results offer new insights into how the flexible motion of giant kelp interacts with nearshore flows, with important implications for the transport of nutrients, spores, and larvae. Accurately parameterizing the time-varying drag of giant kelp in ocean models is essential for better quantifying the influence of kelp forests on coastal hydrodynamics.

  PublisherOA PDFDOI

• Reef Community Productivity and Calcification – Spatial and Temporal Variability in Recovering Coral Reefs

  Journal of Geophysical Research Oceans · 2025-03-01 · 3 citations

  article

  Abstract Coral reefs are currently under threat due to multiple anthropogenic stressors, with increasing temperatures leading to more frequent bleaching events. We assessed reef Net Community Production (NCP) and Net Community Calcification (NCC), measures of reef ecosystem functioning, using a benthic gradient‐flux approach on forereef and lagoon coral reefs recovering from the major 2015–2016 bleaching event in the Chagos Archipelago, Indian Ocean. Hard coral cover at the lagoon was higher (44% vs. 21% at the forereef, 3 years post‐bleaching) and increased by ∼60% at both reefs 6 years post‐bleaching. Calcification, computed using Structure‐from‐Motion photogrammetry, increased by 34%, and rugosity by ∼10% over this period. Biogeochemical measurements show net heterotrophy at both reefs 3 years within the recovery, with the lagoon reef exhibiting particularly high rates. Six years into the recovery process, productivity and calcification rates at the forereef more than doubled compared with the rates 3 years prior. Large day‐to‐day variability was documented. This included a transition in the lagoon reef from net calcification to dissolution within days, despite the long‐term trend of net CaCO 3 accumulation. On the forereef, heterotrophy increased by 51% on cloudy days, while a shift to autotrophy (147% increase in NCP) and 47% higher calcification were found on sunny days that directly followed cloudy days. An internal wave event presumably led to enhanced production on one of the days on the forereef. Our findings highlight the importance of combining long‐term reef health indicators with short‐term measurements of reef functioning to capture the dynamics of reef recovery.

  PublisherDOI

• On the use of simplified geometries to represent turbulent flow over coral reefs

  Journal of Fluid Mechanics · 2025-01-30 · 6 citations

  article

  Hydrodynamic consequences of using simpler geometric shapes to represent coral canopies are examined through a laboratory study. A canopy composed of cylinders is compared with a canopy composed of 3-D-printed, scaled down coral heads in a recirculating flume. Vertical velocity profiles are measured at four horizontal locations for each canopy type, and mean velocity and turbulence statistics are compared both within and above the canopy. A narrow, defined wake on the scale of the canopy element is present behind the cylinder canopy elements that is absent in the coral canopy. There is also a peak in shear stress at the top of the cylinder canopy, likely due to the sharp edge at the top of the cylinder. Above the canopy, however, turbulence statistics and friction velocities behave similarly for both canopy types. Therefore, the results indicate we may reasonably get coral reef drag estimates from canopies with simpler geometric surrogates, especially when the mean free-stream and within-canopy flow speeds are matched to environmental conditions.

  PublisherDOI

• Wave-influenced connectivity and transport in submerged coral canopies

  Coral Reefs · 2025-04-07

  article
  PublisherDOI

• Morphologically driven sedimentation patterns on a coral reef

  Research Square · 2024-04-12 · 1 citations

  preprintOpen access

  Abstract Coral reef sediment research focused on quantifying production sources, suspended sediment, and trapping or accumulation rates, overlooking the role of hydrodynamics and reef morphology in determining these. We used an interdisciplinary approach, focusing on the links between physical features and processes and hypothesized how they affect reef recovery. Typhoon Bopha hit Ngederrak Reef (Palau) in 2012, significantly reducing coral cover. The reef is characterized by spur and grooves (SAGs) and bordered by two tidal channels, but SAGs are not present in its northernmost part, near one of these channels. The reef has recovered in the SAG area, but its recovery was slower in the north. Flow measurements and sediment samples taken in SAG and non-SAG areas were used to calculate the threshold for sediment movement due to mean flows and wave orbital velocities. Sediment on SAGs was mainly suspended by waves, but the direction of net transport was determined by the mean flow. The threshold for sediment movement due to mean flow was reached 80–100% of the time on spurs, in grooves it was reached 60% and 33% of the times during flooding and ebbing tides respectively. This tidal asymmetry suggests that sediment was removed from spurs and transported seaward in grooves to be stored at depth. The steeper slope in grooves (8%) relative to the non-SAG area (4%), favors rubble accumulation and stabilization. This information can help predict localized sediment impacts as well as describing the role of the widely distributed SAG morphology in promoting coral reef recovery.

  PublisherOA PDFDOI

• Bottom Stress and Drag on a Shallow Coral Reef

  Journal of Geophysical Research Oceans · 2024-11-01 · 5 citations

  articleOpen accessSenior author

  Abstract Coral reef roughness produces turbulent boundary layers and bottom stresses that are important for reef metabolism monitoring and reef circulation modeling. However, there is some uncertainty as to whether field methods for estimating bottom stress are applicable in shallow canopy environments as found on coral reefs. Friction velocities () and drag coefficients () were estimated using five independent methods and compared across 14 sites on a shallow forereef (2–9 m deep) in Palau with large and spatially variable coral roughness elements (0.4–1 m tall). The methods included the following: (a) momentum balance closure, (b) log‐fitting to velocity profiles, (c) Reynolds stresses, (d) turbulence dissipation, and (e) roughness characterization from digital elevation models (DEMs). Both velocity profiles and point turbulence measurements indicated good agreement with log‐layer scaling, suggesting that measurements were taken within a well‐developed turbulent boundary layer and that canopy effects were minimal. However, estimated from the DEMs, momentum budget and log‐profile fitting were consistently larger than those estimated from direct turbulence measurements. Near‐bed Reynolds stresses only contributed about 1/3 of the total bottom stress and drag produced by the reef. Thus, effects of topographical heterogeneity that induce mean velocity fluxes, dispersive stresses, and form drag are expected to be important. This decoupling of total drag and local turbulence implies that both rates of mass transfer as well as values of fluxes inferred from concentration measurements may be proportional to smaller, turbulence‐derived values of rather than to those based on larger‐scale flow structure.

  PublisherOA PDFDOI

Recent grants

• Turbulent mixing by nearshore internal bores

  NSF · $231k · 2012–2015

• Collaborative Research: Coupled Carbon and Phosphorus Cycling

  NSF · $368k · 2005–2009

• Collaborative Research: Turbulent fluxes and boundary layer structure due to near-shore internal tides

  NSF · $759k · 2009–2013

• Small-scale flow variability inside branched coral colonies: Computations and experimental verification

  NSF · $439k · 2004–2009

• Collaborative Research: Lateral mixing and dispersion on the inner shelf

  NSF · $597k · 2009–2013

Frequent coauthors

• Jeffrey R. Koseff

  Mechanics' Institute

  133 shared

• Derek A. Fong

  California Public Utilities Commission

  64 shared

• Mark T. Stacey

  University of California, Berkeley

  60 shared

• Oliver B. Fringer

  Stanford University

  58 shared

• C. Brock Woodson

  University of Georgia

  49 shared

• Kristen A. Davis

  Stanford University

  42 shared

• Robert B. Dunbar

  Stanford University

  40 shared

• Geno Pawlak

  Scripps Institution of Oceanography

  40 shared

Education

• Ph.D., Civil Engineering

  Stanford University

  1992

• M.S., Civil Engineering

  University of California, Berkeley

  1987

• B.S., Civil Engineering

  University of California, Berkeley

  1985