Geology Reports⌕ Search

USGS · 70272235

A systematic literature review of forecasting and predictive models of harmful algal blooms in flowing waters

Abstract

Occurrences of harmful algal blooms (HABs) in rivers challenge the belief that rivers are not susceptible to HABs because of their short residence times and fluctuating hydrology. Here we present a systematic literature review of predictive and forecasting models for HABs in flowing waters, including rivers, flowing in-stream reservoirs (e.g., run-of-river reservoirs and lock-and-dam systems) and tidal or estuarine systems with riverine processes. The review aimed to understand current and historical modeling approaches for predicting and forecasting river HABs, without restricting to specific taxa, such as cyanobacteria, or modeling endpoints. The review included 162 articles published over nearly 50 years, covering more than 80 rivers worldwide. Eutrophic, non-wadable rivers with in-stream obstruction were commonly modeled, though diverse environmental characteristics were reported. Most articles used algal biomass or chlorophyll as modeling endpoints, with a quarter using novel or unique endpoints. Algal toxins motivated model development in 23% of the articles, however just 5% used algal toxins as an endpoint. Only 6% of the articles modeled benthic HABs; the rest focused on pelagic HABs. There was no standard model used for modeling river HABs. Process-based models were more common (59%) than data-driven approaches (37%), with model formulations ranging from simple to complex, which contrasts with a lake-focused literature review of HAB models that found data-driven models were more common. Models in river settings shared similar input variables as those previously identified for lakes, such as water temperature, nutrients, and light availability. However, streamflow and other transport metrics took prominence in river models compared to lake models. Algal cell physiology (such as growth, predation, and motility) was routinely included as input data or as mathematical formulations in process-based models and these processes were frequently identified as an important predictor by the articles’ authors. Conversely, data-driven models rarely included these processes, instead using predictors related to environmental conditions, such as nutrients, water quality, water temperature, and streamflow. These important proxy predictors have apparent success with modeling overall algal biomass (irrespective of taxa) whereas other factors, such as those related to algal physiology and other biological processes, are likely responsible for more subtle shifts in community composition. These differences highlight the influence of data availability, especially for processes that are difficult, time-consuming, or expensive to measure, on model development and model outcomes, raising questions about the selection of modeling inputs and endpoints. Challenges to advancing river HAB modeling include the lack of site-specific model inputs representing key processes (e.g., photosynthetic parameters and predation rates), overlooked riverine environments like the benthos and side/back-channel areas, lack of information on environmental settings, and poorly reported model performance metrics. This review emphasizes opportunities for advancing river HAB modeling by learning from well-honed estuarine models, supporting current forecasting and operationalization efforts, and developing common datasets for river HAB model development and evaluation.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Jennifer C. Murphy, Rebecca M. Gorney, Lisa V. Lucas, Jacob Aaron Zwart, Jennifer L. Graham. 2025. A systematic literature review of forecasting and predictive models of harmful algal blooms in flowing waters. https://doi.org/10.1101/2025.09.29.679270

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related USGS reports

Movement mechanisms explain current animal density patterns and predict their reorganization under global change

Aim: To test whether individual movement mechanisms inferred from animal tracking data can be scaled up to explain landscape-scale patterns of population density and improve predictions of population redistribution under future environmental change. Location: Texas Gulf Coast, USA Time Period: 2009-2018 Major Taxa Studied: Whooping Crane (Grus americana) Methods: We parameterized individual-level step-selection functions using 14,898 GPS locations from 22 Whooping Cranes and propagated the resulting movement and habitat-selection mechanisms across the landscape to derive steady-state distributions of space use. We compared these movement-informed predictions with correlative species distribution models fitted to the same data. Predictions were evaluated using withheld tracking observations and fully independent population-level aerial-survey data. We then projected both approaches under sea-level-rise scenarios to assess how future habitat loss and fragmentation alter crane space use. Results: Movement mechanisms derived from individual-level tracking data captured the mechanistic dependence of population density on habitat quality and spatial configuration. When projected across the landscape, these mechanisms reproduced fully independently observed density patterns and outperformed conventional species distribution models. Because predictions arose from movement mechanisms rather than occurrence-environment correlations, movement-informed models also captured the effects of habitat reconfiguration under sea-level rise. They projected pronounced population redistribution and an expansion of core space-use areas of up to 80% which conventional models missed. Main Conclusions: Individual movement mechanisms derived from biologging data can scale up to explain current population structure and predict future redistribution under environmental change. By mechanistically accounting for how habitat configuration constrains accessibility, movement-informed models reveal severe impacts of fragmentation that are missed by conventional distribution models. Rapidly expanding biologging datasets therefore offer a scalable basis for connecting individual behavior to macroecological patterns and improving biodiversity forecasts in changing landscapes.

BioRxiv↗

The hidden prior: Variance constraints under data augmentation

Data augmentation is now a standard device across capture–recapture and occupancy analysis: adding a fixed number M of all-zero encounter histories replaces a model of unknown dimension with one of fixed dimension. Although M is often treated as a computational tuning choice, it also specifies a finite superpopulation and hence a binomial support constraint on the number of undetected individuals. In a Bayesian implementation that constraint appears as an induced prior; in a likelihood implementation it is the same finite-support assumption reached by another route. That the Bernoulli specification for the inclusion indicators induces a binomial prior on abundance is established ( Schofield & Barker 2014 ); our concern is what that choice costs in estimated uncertainty. We develop the argument using a simple closed-population abundance estimation problem. We show that augmented occupancy and Huggins conditional-likelihood analyses give numerically identical point estimates of N^ once M is sufficiently large. Their uncertainty estimates, however, need not agree. We distinguish two sources of discrepancy. First, when M is small relative to the number of undetected individuals, the finite binomial ceiling truncates the likelihood or posterior and suppresses uncertainty. Second, once that ceiling no longer binds, Taylor-series (Delta-method) approximations still understate variance, because the quantity of interest is a strongly non-linear function of the estimated parameters and local linearization does not reproduce its curvature. Gauss–Hermite quadrature on the unconstrained logit scale recovers much of the shortfall and approaches the MCMC posterior benchmark, though a small residual remains that does not close as M grows, reflecting the distinction between asymptotic likelihood theory and finite-sample Bayesian inference. Neither mechanism is peculiar to abundance estimation: the first follows from the augmented representation itself, the second from any derived quantity that is a non-linear function of estimated parameters. We close with framework-specific guidance for choosing M.

BioRxiv↗

Southern (California) sea otter population status and trends at San Nicolas Island, 2023–winter 2026

The southern sea otter ( Enhydra lutris nereis ) population at San Nicolas Island, California, has been monitored annually since the translocation of 140 sea otters to the island was completed in 1990. Monitoring efforts have varied in frequency and method across years. In 2017, in accordance with the National Defense Authorization Act for Fiscal Year 2016, the U.S. Navy and the U.S. Fish and Wildlife Service formally initiated a sea otter monitoring and research plan to determine the effects of military readiness activities on the growth or decline of the southern sea otter population at San Nicolas Island. The monitoring program, at its basic level, includes quarterly seasonal surveys of population abundance, distribution, and foraging activity. This report presents data from the program with a focus on the recent three years from winter 2023 through winter (February) 2026. From 2023 to 2026, we measured an 8.1-percent per annum decrease in population abundance (95-percent confidence interval =1.1–14.6 percent), with 106 total individuals counted as of February 2026. Historically, sea otter habitat usage at San Nicolas Island was concentrated on the west end of the island. Between 2017 and 2019, we observed increased seasonal usage of the north and south sides of the island, and in 2020-2022, a large (approximately 30-40 individuals) group of sea otters (raft) took up residence off the east end. During 2023-2026 the east end raft disappeared, and sea otters returned to their historical habitat usage patterns at the west end of the island. Foraging data were collected from summer 2023 to winter 2026 on a total of 461 foraging dives in 32 foraging bouts, and the majority of identified prey on successful dives (n=325) were sea urchins (124) followed by snails (48), bivalves (41) and crabs (23). One lobster and one octopus were also identified among the sea otter prey items. We combined these data with data from 2020-2022 to estimate overall energy intake rates that averaged 7.7 kilocalories per minute (95-percent credible interval =6.6–9.1 kilocalories per minute). These results can be useful to the planning of future monitoring and research of sea otters at San Nicolas Island.

BioRxiv↗