Lake biogeochemistry is influenced by both internal processes, such as water-column stratification, and external pressures, including nutrient inputs from streams draining surrounding watersheds. In Central America, Lake Atitlán is a caldera lake supported by a long-term freshwater monitoring program that offers a valuable opportunity to examine biogeochemical dynamics in a tropical mountain watershed. In this study, we analyzed data from 2017-2024 to characterize spatiotemporal patterns in water chemistry across tributary rivers and sites in the lake, and (2) assess seasonal variability in water quality in both rivers and the lake. We present data from rivers that drain into Lake Atitlán, including San Francisco, Catarata, and San Buenaventura, as well as from two lake sites: San Buenaventura, a shallow nearshore site at 10 m depth, and Panajachel, a deep pelagic site at 100 m depth. Across rivers, concentrations of nitrate and nitrite (NO₃+NO₂), ammonium (NH4+), soluble reactive phosphorus (SRP), and total phosphorus (TP) showed no consistent differences between the dry and rainy seasons. NO₃+NO₂ concentrations were generally higher in the San Buenaventura and Catarata rivers than in San Francisco, whereas SRP and TP concentrations were highest in San Francisco. In contrast, conductivity and total dissolved solids were seasonal, with higher values during the dry season and consistently greater in San Francisco. Most analytes did not display trends; however, NO₃+NO₂ concentrations increased over time in San Buenaventura and San Francisco. Physicochemical patterns in the lake were heterogeneous. In Panajachel, the lake exhibited monomictic mixing, with stratification beginning in February, a fully developed thermocline by April, and complete water-column mixing each January. Dissolved oxygen varied with depth, with the highest values in the epilimnion and metalimnion and the lowest in the hypolimnion. In contrast, San Buenaventura displayed polymictic mixing, with dissolved oxygen more evenly distributed throughout the water column. Nutrients in Panajachel were typically lowest in the epilimnion and accumulated in the hypolimnion, while at San Buenaventura, nutrients were more uniformly distributed across depths. Insights into freshwater quality can inform management strategies that protect the lake’s ecological integrity.