Clinical coordination mechanisms (CCMs) have become key tools in healthcare networks for improving coordination between primary care (PC) and secondary care (SC) and are particularly relevant in health systems with highly fragmented healthcare provision. However, their implementation has been little studied to date in Latin America and particularly in Colombia. This study analyses the level of knowledge and use of CCMs between care levels and their changes between 2015 and 2017 in two public healthcare networks in Bogotá, Colombia. Comparison of two cross-sectional studies based on surveys among PC and SC doctors working in their networks (174 doctors per network/year). The COORDENA questionnaire was used for measuring knowledge concerning CCMs and the frequency of use and difficulties involved in using referral/reply letters (R/RLs) and hospital discharge reports (HDRs). Descriptive bivariate analysis and Poisson regression models with robust variance were used for analysing differences between networks and years. The results for both networks and years revealed greater knowledge and use of information coordination mechanisms than those regarding clinical management coordination (though their knowledge increased in 2017). Although widely known and used, significant problems regarding infrequent and late receipt of RLs and HDRs in PC as well as the poor quality of their contents limits their effective use, which may affect the quality of care. Strategies are required to improve CCMs use.