# Exploring the Spectral Variability of Estonian Lakes Using Spaceborne Imaging Spectroscopy
## 2 Materials and Methods  
### Study Area  
This study focuses on two of the largest and ecologically most significant freshwater bodies in Estonia: Lake Peipsi and Lake Vortsjarv. These lakes are key components of Estonia's inland water system and serve critical roles in regional biodiversity, hydrology, and socio-economic activities such as fishing and recreation [54]. Lake Peipsi is located on the eastern border of Estonia (shared with Russia) and is the fourth biggest lake in Europe, covering an area of approximately 3555 km\({}^{2}\)[55]. The lake is part of a transboundary catchment and is hydrologically connected to the Narva River, which flows into the Gulf of Finland. It is divided into three parts: the mesotrophic Lake Peipsi _sensu strictu_ (s.s.) in the north, the hypertrophic Lake Pihkxus in the south, and their connection and river-like eutrophic Lammijarv [56]. Different water types can be observed in the lake: clearest and deepest water in the northern part, turbid and brownish water near the river Emajogi inflow, and phytoplankton-rich water in Lammijarv and Lake Pihkxus [57]; in the summertime, cyanobacterial blooms may be present throughout the entire lake [58]. Rivering transport constitutes the primary pathway for nutrient input into the lake. Over 80% of phosphorus and nitrogen compounds are introduced into Lake Peipsi via the Velikaya River, which carries treated wastewater from the Russian city of Pskov, and the Emajogi River, which receives treated wastewater from the Estonian city of Tartu [59]. Lake Peipsi has a shallow basin with an average depth of 7.1 m, which makes it sensitive to nutrient loading and climatic fluctuations [60]. Lake Peipsi is ecologically diverse and serves as a critical habitat for numerous fish and bird species. However, the lake has also been subject to eutrophication and water quality degradation due to agricultural runoff and historical pollution [61]. The average values recorded in the lake from the national monitoring programme [62] in the period 2020-2024 for the main bio-optical components are: Chl-a 27 \(\pm\) 21 mgm\({}^{-3}\), TSM 10 \(\pm\) 8 gm\({}^{-3}\), and CDOM (443 nm) 3 \(\pm\) 1.4 m\({}^{-1}\). Lake Vortsjarv, located in south-central Estonia, is the largest lake entirely within the country's borders, with a surface area of about 270 km\({}^{2}\). It is significantly shallower than Lake Peipsi, with an average depth of 2.8 m. Lake Vortsjarv is a very turbid, well-mixed, eutrophic, and non-stratified lake with high levels of phytoplankton, concentration of TSM, and absorption coefficient of CDOM. The lake is part of the Emajogi River system, which connects it to Lake Peipsi. Lake Vortsjarv is also a vital freshwater resource, it provides habitats for several protected species, and plays a key role in regional hydrological dynamics [63]. Due to its shallow nature, it is highly vulnerable to climatic variability, particularly changes in precipitation and evaporation rates. The littoral zone of Lake Vortsjarv is covered by a wide belt of aquatic macrophytes, dominated by _Phragmites australis_, common reed, and other helpbytes; notably, the southwestern region--thanks to its relative protection from prevailing winds--exhibits the highest density of aquatic vegetation [64]. In addition, it is characterized by ice cover that lasts on average more than 100 days, approximately from November to April [65]. The average values recorded in the lake from the national monitoring programme [66] in the period 2020-2024 for the main bio-optical components are: Chl-a 31 \(\pm\) 14 mgm\({}^{-3}\), TSM 18 \(\pm\) 12 gm\({}^{-3}\), and CDOM (443 nm) 2.8 \(\pm\) 2 m\({}^{-1}\). Together, these two lakes provide a representative context for examining limnological processes, environmental changes, and human impacts in Northern European freshwater systems. Ancillary variables such as lake surface water temperature, wind speed, and precipitation, retrieved from the ERA5 reanalysis dataset via the Copernicus Climate Data Store [67], supported the description of the study area.