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Decomposition of plant debris is a critical process during the filling phase of water reservoir. Here we investigated the impact of decomposition of the plant species (Cytisus scoparius, Pteridium aquilinum and Juncus effusus) in the Alaco reservoir (southern Italy). To simulate lake ecological conditions, a microcosm experiment was carried-out for 100 days with litters incubated in water lake in aerobic conditions in the light at two temperatures (+12 °C and +24 °C). Litter types were characterized by classic proximate chemical analyses (total C and N, labile C, cellulose and lignin content, C/N and lignin/N ratios) and, at molecular level, by solid-state 13C CPMAS NMR. Water quality was monitored through pH, electrolytic conductivity, DOC, BOD5 and dissolved oxygen. Decomposition was more rapid for C. scoparius, intermediate for J. effusus and slower for P. aquilinum. After 100 days of decomposition for all litter type the O-alkyl-C region, associated with sugars and polysaccharides, decreased and the aliphatic alkyl-C region increased for C. scoparius and P. aquilinum. Immediately after litter submergence, DOC and BOD5 dramatically increased, reaching high values for P. aquilinum and C. scoparius. However, after 100 days of incubation, DOC concentration sharply decreased reaching values usually below 50 mg l−1, and after 10 days of incubation BOD5 values dropped to values close to zero. Although carried out in laboratory, the experiment showed that submerged plant litter during decomposition produces a short-term changes of water quality that rapidly returns to background level.