System level indices from ecosystem network analysis (ENA) were calculated for the carbon flow networks representing Lake Santo and Lake Scuro ecosystems. Long-term data were used to construct the time series of networks representing carbon flows in the two ecosystems (Lake Santo: 1973, 1991, 2001, 2003 and 2007-2009; Lake Scuro: 1986, 1989-1994, 1998, 2003 and 2007-2009). The following indices were calculated: H - diversity of flows; AMI - average mutual information; HC - residual diversity; DC - development capacity; A - ascendency; O - overhead; TST - total system throughput; P - primary productivity (of phytoplankton); TOM - total organic matter; IR - flow redundancy; IC - internal connectance (data in file ScottiM_2019_lakes-indices.zip).All flows in the networks constructed to model carbon circulation in Lake Santo and Lake Scuro are reported. The time series includes 7 networks in the case of Lake Santo (1973, 1991, 2001, 2003 and 2007-2009) and 12 networks for Lake Scuro (1986, 1989-1994, 1998, 2003 and 2007-2009). Lake Santo is composed of 26 compartments (23 living and 3 non-living) while Lake Scuro has 22 compartments (19 living and 3 non-living). Four types of flows are summarized: (i) input from outside the system (i.e. photosynthesis or carbon flows due to leaves or other organic materials that contribute to the standing stocks of water DOC and water POC); (ii) export of still usable carbon outside system's boundaries (i.e. carbon burial into the sediment from benthic POC); (iii) respiration/dissipation; and (iv) inter-compartmental exchanges among compartments composing the system (i.e. flows from prey/resources to predators/consumers). All flows are in grams of carbon per cubic meter per year. Table columns represent: (i) donor compartments; (ii) recipient compartments; (iii) short explanation of the processes represented; (iv) strength of the flows (i.e. amount of carbon transferred) during the various years of the time series (i.e. 7 years for Lake Santo and 12 years for Lake Scuro) (data in file ScottiM_2019_lakes-dataset.zip).