Due to global warming and increasing water eutrophication, understanding in-lake relationships is paramount to prevent excessive pollution and further negative changes in lakes. The physico-chemical and biological parameters, as well as nutrient variabilities, both temporal and vertical (in the water column), were studied in the largest Łęczna-Włodawa lake. The study was conducted during two consecutive water years, from November 2015 to September 2017. The non-parametric Kruskal–Wallis ANOVA, test H was used to detect variability between years, and among seasons and lake depths in water temperature, electrical conductivity, pH, ORP, concentration of dissolved oxygen as well as concentration of NO3−, PO43−, TP and chlorophyll a. One-way analysis of variance (ANOVA) was used to detect any differences in Secchi depth (SD) and concentration of NH4+, NO2−, and TN. Ordination techniques: Detrended correspondence analysis (DCA), and Principal Components Analysis (PCA) were used to describe the relationships among 13 environmental variables and distribution of samples. Results showed significant differences (P < 0.05) between two years of the study for most variables except of water temperature, visibility, concentration of PO43−, TN and TP, which corresponded with highly different weather conditions in both years. All of the tested variables, except for nutrients, differed significantly among seasons. Most parameters showed fluctuation in depth, especially in summer and in winter, despite the fact that no hypolimnion or long-lasting thermocline was observed in the study period. However, variability of Chl-a was statistically significant only. The results emphasized complex and multi-directional relations between tested variables, dependent on both external (catchment) and internal (in-lake) processes.