Canadian ecosystems play a vital role in regulating the climate by exchanging greenhouse gases (GHGs) across natural and managed forests, wetlands, croplands, grasslands, and urban green space. Therefore, it is crucial to continuously monitor GHG fluxes within these diverse ecosystems. Varying approaches in producing and handling eddy-covariance (EC) flux data can result in diverse, non-standardized datasets, hindering cross-site comparisons, and limiting data utility beyond the ecosystem-scale. Our EcoFlux data-cleaning pipeline applies consistent approaches to EC data quality control, gap-filling, and flux partitioning allowing comparability across sites. The pipeline methodology is designed to be simple to implement, with minimal programming required. Scripted mainly in Matlab and R, it incorporates resources and algorithms based on FLUXNET and other regional networks, as well as the REddyProc R-package. Recent efforts are working on revitalizing CanFlux, a national network dedicated to measuring and understanding carbon, water, energy, and other GHG fluxes. Using the Ecoflux pipeline, standardized data from this network will support climate research; improve and validate carbon models like CLASSIC, CBM-CFS3, and CaMP; and ultimately inform policy changes on climate mitigation and adaptation, on both national and international levels. The CanFlux mission is long-term data curation on a national scale, with the help of sustained financial support to maintain continuous data collection, increasing the security of Canada’s monitoring capacity and flux science community.