Abstract. Seasonal variation in water table depth (WTD) determines the balance between aggradation and degradation of tropical peatlands. Longer dry seasons together with human interventions (e.g. drainage) can cause WTD drawdowns making tropical peatland C storage highly vulnerable. Better predictive capacity for effects of WTD on net CO₂ exchange is thus essential to guide conservation of tropical peat deposits. Mathematical modelling of basic eco-hydrological processes under site-specific conditions can provide such predictive capacity. We hereby deploy a process-based mathematical model ecosys to study effects of seasonal variation in WTD on net ecosystem productivity (NEP) of a drainage affected tropical peat swamp forest at Palangkaraya, Indonesia. Simulated NEP suggested that the peatland was a C source (NEP ~ −2 g C m⁻² d⁻¹, where a negative sign represents a C source and a positive sign a C sink) during rainy seasons with shallow WTD, C neutral or a small sink (NEP ~ +1 g C m⁻² d⁻¹) during early dry seasons with intermediate WTD and a substantial C source (NEP ~ −4 g C m⁻² d⁻¹) during late dry seasons with deep WTD from 2002 to 2005. These values were corroborated by regressions (P < 0.0001) of hourly modelled vs. eddy covariance (EC) net ecosystem CO₂ fluxes which yielded R² > 0.8, intercepts approaching 0 and slopes approaching 1. We also simulated a gradual increase in annual NEP from 2002 (−609 g C m⁻²) to 2005 (−373 g C m⁻²) with decreasing WTD which was attributed to declines in duration and intensity of dry seasons following the El Niño event of 2002. This increase in modelled NEP was corroborated by EC-gap filled annual NEP estimates. Our modelling hypotheses suggested that (1) poor aeration in wet soils during shallow WTD caused slow nutrient (predominantly phosphorus) mineralization and consequent slow plant nutrient uptake that suppressed gross primary productivity (GPP) and hence NEP (2) better soil aeration during intermediate WTD enhanced nutrient mineralization and hence plant nutrient uptake, GPP and NEP and (3) deep WTD suppressed NEP through a combination of reduced GPP due to plant water stress and increased ecosystem respiration (R_e) from enhanced deeper peat aeration. These WTD effects on NEP were modelled from basic eco-hydrological processes including microbial and root oxidation-reduction reactions driven by soil and root O₂ transport and uptake which in turn drove soil and plant carbon, nitrogen and phosphorus transformations within a soil-plant-atmosphere water transfer scheme driven by water potential gradients. Including these processes in ecosystem models should therefore provide an improved predictive capacity for WTD management programs intended to reduce tropical peat degradation.