The catchment of Lake Alaotra, a large shallow lake (surface is 200 km², maximum depth 2 m) in the Malagasy highlands, is a region where the grassland dominated landscape is dotted by major gullies called “lavaka”, which has historically been claimed to lead to high erosion rates. Sedimentary archives in lakes such as Lake Alaotra could be of great help to resolve questions about the natural versus anthropogenic influences on the changing landscape, provided that we understand carbon sources and sinks within the lake, as well as the connection with the surrounding landscape through the input of material via inflowing water. Here, we provide a first comprehensive survey of the carbon (C) biogeochemistry of the Lake Alaotra system. We investigated the seasonal variability of the concentrations and stable isotope C ratios of inorganic and organic C pools, as well as a range of other relevant proxies, including physico-chemical parameters, dissolved CO₂ and CH₄ concentrations, total alkalinity, and Chl-a (chlorophyll a) from spatially distributed sampling and seasonal monitoring of several rivers. While rivers were found to carry high total suspended matter (TSM) loads with a modest particulate organic C (POC) content, the lake itself and its outflow were characterised by much lower TSM values and high %POC (relative contribution of POC to TSM). The POC concentration of the outflow (13.0 ± 7.7 mg L^-1) was substantially higher than in the inflowing water (1.9 ± 2.1 mg L^-1), and δ¹³C values were also distinct between inflowing water (-24.6 ± 1.8 ‰) and the lake (-26.5 ± 2.1 ‰) or its outflow (-25.2 ± 1.4 ‰). Similarly, the lake outflow was surprisingly rich in DOC (9.5 ± 1.4 mg L^-1) compared to inflowing water (2.6 ± 1.1 mg L^-1). This indicates that the lake and its surrounding wetlands act as a substantial source of additional organic C which is exported downstream. The CO₂ and CH₄ concentrations in inflowing and outflowing rivers were substantially higher than in lake waters, and peaked during the rainy season due to lateral inputs from wetlands. However, sources of POC and DOC were uncoupled: δ¹³C data were consistent with marsh vegetation being the main source of net DOC inputs, while phytoplankton was expected to be an important source of POC in the lacustrine waters. Lake suspended matter has low POC/Chl-a ratios (143–564), high %POC (10 to 29 %), and δ¹³C values around 20 ‰ lower than the dissolved inorganic C (DIC) pool (-26.5 ± 2.1 ‰ versus -6.7 ± 1.6 ‰). Despite the importance of phytoplankton production to the lake POC pool, the lake acted as a net source of CO₂ to the atmosphere, likely due to the high C inputs from the surrounding marshes, and sediment respiration considering the shallow water depth. Nevertheless, the pCO₂ in the surface waters of the lake was lower than in the inflowing and outflowing rivers, possibly reflecting the impact of phytoplankton production (CO₂ assimilation), although also reflecting degassing to the atmosphere. The biogeochemical functioning of Lake Alaotra differs substantially from the large and deeper East African (sub)tropical lakes and was similar to lakes surrounded by flooded forest in the Congo River basin, likely due to a combination of its large surface area and shallow water depth, and the large extent of surrounding wetlands and floodplains. It acts as an abrupt element in the land-ocean gradient of the catchment, whereby the biogeochemical characteristics of the Maningory River (i.e., the lake outflow) are strongly determined by processes taking place in Lake Alaotra and its wetlands, rather than being reflective of characteristics and processes higher up in the catchment.