Macrophytes are important sources of dissolved organic carbon (DOC) to littoral zones of lakes, but this DOC is believed to be mostly refractory to bacteria, leading to the hypothesis that bacterial metabolism is different in littoral and pelagic zones of a large subtropical shallow lake. We tested this hypothesis by three approaches: (I) dissolved inorganic carbon (DIC) accumulation in littoral and pelagic water; (II) O(2) consumption estimate for a cloud of points (n = 47) covering the entire lake; (III) measurement of O(2) consumption and CO(2) accumulation in dark bottles, pCO(2) in the water, lake-atmosphere fluxes of CO(2) (fCO(2)) and a large set of limnological variables at 19 sampling points (littoral and pelagic zones) during seven extensive campaigns. For the first two approaches, DIC and O(2) consumption were consistently lower in the littoral zone, and O(2) consumption increased marginally with the distance to the nearest shore. For the third approach, we found in the littoral zone consistently lower DOC, total phosphorus (TP), and chlorophyll a, and a higher proportion of low-molecular-weight substances. Regression trees confirmed that high respiration (O(2) consumption and CO(2) production) was associated to lower concentration of low-molecular-weight substances, while pCO(2) was associated to DOC and TP, confirming that CO(2) supersaturation occurs in an attempt to balance phosphorus deficiency of macrophyte substrates. Littoral zone fCO(2) showed a tendency to be a CO(2) sink, whereas the pelagic zone showed a tendency to act as CO(2) source to the atmosphere. The high proportion of low-molecular-weight, unreactive substances, together with lower DOC and TP may impose lower rates of respiration in littoral zones. This effect of perennial stands of macrophytes may therefore have important, but not yet quantified implications for the global carbon metabolism of these lakes, but other issues still need to be carefully addressed before rejecting the general belief that macrophytes are always beneficial to bacteria.