This study analyses the effects of the interplay between climate seasonality and hydrogeomorphic (HGM) lake features on dissolved organic matter (DOM) properties in two neighbouring shallow lakes of Andean Patagonia with different connectivities. The survey was conducted over three years at the end of the wet and dry seasons, assessing the seasonal and interannual variation of dissolved organic carbon (DOC) concentration, whole-lake DOC mass, and DOM quality, through chromophoric and fluorescent DOM (CDOM and FDOM, respectively) properties. During the wet season (fall-winter), precipitation and runoff increased water discharge, water level, and inputs of terrestrial DOM with high aromaticity, humic content, and high molecular weight in both lakes. Contrastingly, during the dry season (spring-summer), in which photodegradation promoted by high irradiance and stagnant conditions drove DOM transformation, nonhumic, low-molecular-weight DOM prevailed. Both lakes displayed synchronicity in their DOC mass and CDOM and FDOM properties, indicative of similar responses to climate forcing, although the overall impact was modulated by their HGM features. Conversely, DOC concentration showed asynchronous responses between lakes, due to the higher intensity of the dilution or evapoconcentration processes in the connected lake, highlighting that DOC concentration is not always sensitive to climate-driven forces. Overall, this study emphasizes the importance of variables other than DOC concentration, like whole-lake DOC mass, DOM quality, and HGM features, to better understand the effect of climate variability on DOM dynamics. Our results allow inferring the potential impact of an environmental scenario characterized by lower precipitation and sustained warming on DOM dynamics in Northern Andean Patagonia.