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Abstract Near‐term ecological forecasts provide resource managers advance notice of changes in ecosystem services, such as fisheries stocks, timber yields, or water quality. Importantly, ecological forecasts can identify where there is uncertainty in the forecasting system, which is necessary to improve forecast skill and guide interpretation of forecast results. Uncertainty partitioning identifies the relative contributions to total forecast variance introduced by different sources, including specification of the model structure, errors in driver data, and estimation of current states (initial conditions). Uncertainty partitioning could be particularly useful in improving forecasts of highly variable cyanobacterial densities, which are difficult to predict and present a persistent challenge for lake managers. As cyanobacteria can produce toxic and unsightly surface scums, advance warning when cyanobacterial densities are increasing could help managers mitigate water quality issues. Here, we fit 13 Bayesian state‐space models to evaluate different hypotheses about cyanobacterial densities in a low nutrient lake that experiences sporadic surface scums of the toxin‐producing cyanobacterium,Gloeotrichia echinulata. We used data from several summers of weekly cyanobacteria samples to identify dominant sources of uncertainty for near‐term (1‐ to 4‐week) forecasts ofG. echinulatadensities. Water temperature was an important predictor of cyanobacterial densities during model fitting and at the 4‐week forecast horizon. However, no physical covariates improved model performance over a simple model including the previous week's densities in 1‐week‐ahead forecasts. Even the best fit models exhibited large variance in forecasted cyanobacterial densities and did not capture rare peak occurrences, indicating that significant explanatory variables when fitting models to historical data are not always effective for forecasting. Uncertainty partitioning revealed that model process specification and initial conditions dominated forecast uncertainty. These findings indicate that long‐term studies of different cyanobacterial life stages and movement in the water column as well as measurements of drivers relevant to different life stages could improve model process representation of cyanobacteria abundance. In addition, improved observation protocols could better define initial conditions and reduce spatial misalignment of environmental data and cyanobacteria observations. Our results emphasize the importance of ecological forecasting principles and uncertainty partitioning to refine and understand predictive capacity across ecosystems.