Integrated rice-shrimp ponds (IRSPs) have periods of low oxygen and high nutrient loads which may have a critical effect on both shrimp survival and water quality in adjacent waterways. To understand drivers of poor water quality, this study examined sediment nutrient pathways at two IRSPs. The study showed that the IRSPs had low denitrification efficiency. However, denitrification rates were significantly positively correlated with chlorophyll a concentrations, suggesting carbon availability was a key driver of denitrification. Dissolved nutrient concentrations in the water column were relatively high despite low sediment nutrient effluxes. Given the low sediment nutrient effluxes, and low nitrogen (N) removal by denitrification, the high nutrient loads were likely derived from incoming water. Therefore, the IRSPs were net nutrient removal mechanisms, rather than contributing to eutrophication in adjacent waterways. There also appears to be scope to enhance denitrification for increased N removal, via carbon addition, and hence improve water quality.