Abstract Spatial and temporal patterns of nutrient (nitrate-N, ammonia-N and phosphate) concentrations in the Nong Han water column were examined during the dry (January – May) and wet (August – October) seasons in 2001. Low nitrate-N concentrations in the water were common. High ammonia-N concentrations were found on all occasions, but particularly in the early wet season. Phosphate concentrations in the water column were very high. The very low nitrate-N and low ammonia-N concentrations (in early dry, late dry and late wet seasons), and low phosphate concentrations (in the early dry season) were attributed to assimilation by dense stands of macrophytes, in particular submerged types during the low water season. Additionally, higher nitrate-N concentrations found in the late wet season might be related to increases in the water level and nitrification activity at the sediment–water interface. The very high ammonia-N and phosphate concentrations in the water during the early wet season possibly reflect run-off from agricultural areas in the Nong Han catchment and the regeneration of ammonia-N and phosphate from recently degraded organic matter (particularly decaying macrophytes) in the surface sediment layer. Also, higher phosphate concentrations in the bottom water of most samples in the late dry and late wet seasons were attributed to temporary anaerobic conditions caused by submerged macrophyte decomposition and aerobic conditions, respectively. These hypotheses are consistent with dissolved oxygen and pH conditions found in both seasons.