Climatic and Topographic Controls on Machine Learning-Based Rainfall Forecast Errors in a Tropical Monsoon Basin

Conventional evaluations of rainfall prediction models rely on average accuracy, often masking the conditions, locations and causes of model failure and reduced reliability. This study proposes a paradigm shift from conventional average-accuracy benchmarking toward failure-aware forecast-error diagnosis in the Bengawan Solo River Basin, a tropical monsoon river basin in Indonesia with moderate topographic gradients (grid elevations span ≈ 300–650 m). Methodologically, forecasts from previously published models are treated as fixed inputs and their errors are modelled as the response variable, so the analysis diagnoses when and where models fail rather than retraining them. By treating forecast errors as response variables, rather than as random residuals, this study analyses 345,180 model–grid records–month records from ten individual models (RF, XGB, LGBM, SVR, MLP, LSTM, GRU, TCN, CNN, Transformer) and one best ensemble model (Ensemble_Q, a stacking of RF, XGB, SVR, MLP, LGBM, LSTM, GRU, TCN, CNN, Transformer) against observed CHIRPS (Climate Hazards Group InfraRed Precipitation with Station data) precipitation, seasonal phase, ENSO and IOD regimes (El Niño–Southern Oscillation and Indian Ocean Dipole, respectively), the MJO index (Madden–Julian Oscillation) as an additional analysis, and elevation as a topographic control, using log-error models, high-error logistic regression, interaction tests, and block bootstrap validation (N = 1000), false discovery rate, and spatial statistics. Results indicate that prediction errors are not random but are systematically controlled: the Transition II phase increases log-error by 245% (pooled log-error model) and raises the odds of a high-error event roughly 40-fold relative to the dry season; La Niña conditions amplify errors by 41% and the odds of a high-error event by 3.3 times (though this ENSO signal is largely entangled with co-occurring Negative-IOD months), and every 100 m increase in elevation increases errors by 26%, with errors forming distinct spatial clusters (Moran’s I = 0.78; p = 0.001). Ensemble_Q outperforms the baseline on an aggregate basis (mean absolute error, MAE = 54.10 mm) but still experiences error amplification under these conditions, while spatial deep-learning architectures (TCN, CNN, Transformer) prove most vulnerable to elevation gradients. All major patterns persisted across variations in thresholds, model subsets, ENSO definitions, multiplicity corrections, and bootstrapping. These findings confirm that superior mean accuracy does not guarantee operational reliability, and that conditional failure diagnosis is an essential complement to benchmarking rainfall predictions in tropical monsoon regions.