Understanding the drivers and how they affect ecosystem metabolism is essential for developing effective management policy and plans. In this study, net ecosystem production (NEP), ecosystem respiration (R), and gross primary production (GPP) rates were estimated in relation to physicochemical, hydrological, and meteorological variables in La Salada (LS) and Sauce Grande (SG), two shallow lakes located in an important agricultural region with water management. LS is a mesosaline, mesotrophic-eutrophic lake, whereas SG is a hyposaline and eutrophic lake. GPP and R showed daily and seasonal variations, with R exceeding GPP during most of the study period in both lakes. Net heterotrophic conditions prevailed during the study period (NEP LS: −1.1 mmol O2 m−2 day−1 and NEP SG: −1.25 mmol O2 m−2 day−1). From data analysis, the temperature, wind speed, and lake volume are the main drivers of ecosystem metabolism for both lakes. Despite the significant differences between the two lakes, the NEP values were similar. The different hydrological characteristics (endorheic vs. flushing lake) were crucial in explaining why the two different systems presented similar ecosystem metabolic rates, emphasizing the importance of water management.