The degradation of organic matter from terrestrial systems in inland waters is a critical component of the global carbon cycle. However, the multiple controls on organic matter decay rates hamper predicting the fate of organic matter in freshwaters and therefore, the amount of organic matter mineralized and released to the atmosphere during its transport remains uncertain. To push forward our understanding on the reactivity patterns and on the existence and location of organic matter degradation pulses across the continuum of inland waters, an assessment is needed at two contrasted scales: from the molecular level up to the regional scale. On the one hand, it is still a major challenge to understand the links between biodegradation kinetics and the myriad of compounds comprising organic matter. The application of degradation models to data sets on organic matter composition from molecular-based analytical techniques may grant a better understanding on the mechanistic basis of organic matter degradation kinetics in the near future. On the other hand, it is a foremost need to determine the distribution of these reactivity patterns in the landscape and thus to identify the main factors controlling organic matter at larger scales. We aim to highlight the main modulators of organic matter decay rates identified in recent studies, such as water residence time, and to underline the links identified so far between organic matter composition and these modulators. We explore the different kinetic models used to study organic matter degradation and the molecular compounds driving these degradation patterns. Recent evidence on the landscape controls of organic matter composition across regional gradients are presented and linked to the distribution of decay rates across freshwater ecosystems. We then show the relationship between organic matter decay rates and water retention time across freshwaters ecosystems and compare the turnover time of organic matter in freshwater with terrestrial and marine ecosystems.