Lake Titicaca is the largest freshwater lake in South America and one of the highest and oldest of the world's large lakes, but very little of its ecology is known. We report results from a study on the spatial variation of decomposition rate of Schoenoplectus tatora in Inner Puno Bay affected by direct wastewater discharges. The aims of the research were: (1) to evaluate the effect of benthos exclusion and the influence of other environmental factors on decomposition and (2) to map the decomposition rate in order to describe the spatial heterogeneity in the water body. We carried out the study at 21 sampling points using both fine-meshed and coarse-meshed litterbags to exclude and to allow detritivore action, respectively. Decomposition was on the average faster in the former than in the latter treatment. However, the difference decreased with increasing detritivore abundance, and reversed in the most densely populated waters of the bay. Coupled spatial dependence of the decomposition rate and temperature was observed. Both variables were related with the distance from the wastewater discharges, suggesting that thermal pollution constrains the decomposition rate within the inner bay. Detritivores did not change the general trend imposed by temperature, but their presence increased the spatial heterogeneity of the process.