ABSTRACT Lakes are widely distributed across Costa Rica, from coasts to the highest elevation regions, and located in the main terrestrial biomes. However, updated biogeochemical information about the main types of lakes is still lacking. We present comparative biogeochemistry (water chemistry, stable isotopes, and picoplankton) for a coastal lake (Lake Madre de Dios, LMD), a volcanic lake (Lake Barva, LB), and a glacial lake (Lake Ditkevi, LD). Sampling was conducted between February-November 2022 including dry and rainy seasonal conditions. Hydrological and chemical conditions were evaluated using water and carbon stable isotopes, dissolved organic matter (DOM), major ions, and microbiota analysis. Isotopic data (δ18O, δ13CDIC) confirmed lower evaporative losses for the maar and tarn lakes and productivity response to precipitation inputs. Excitation/Emission matrices confirmed the prevalence of fulvic and humic acids in the coastal and glacial lakes, mainly aromatic proteins and soluble microbial by-products in the volcanic lake. Picophytoplankton (PPP, ∼0.2 to 10 μm) was mainly represented by phycocyanin-rich picocyanobacteria (PC-Pcy) events in the three lakes, but maar and tarn lakes had more representation of phycoerythrin (PE-Pcy) events. We confirmed fluctuations in PPP cell abundance in the lakes lower than in temperate lakes. Like in other eutrophic lakes, Pcy also dominated over picoeukaryotes (Peuk) algae abundance. This work seeks to promote adopting an ecosystem approach to study the biogeochemical functioning of tropical lakes using the combination of chemical, hydrological, and biological data and to provide baseline information for future studies (e.g., climate change and pollution impacts) on tropical lakes of Costa Rica.