INTRODUCTION Research of large lakes is highly complex as such lakes expand over a large area and are affected by an enormous number of different climatic and environmental factors (Blenckner, 2008). Various specific indicators and indexes are needed to facilitate the understanding of the state (and its changes) of large lakes. The zooplankton : phytoplankton biomass ratio ([MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII]) largely reflects the type (effectiveness) of the food web in a water body and hence the nature of the ecosystem. Indirectly, it characterizes dominating groups in phyto- and zooplankton, feeding relationships between them and fish, as well as the pressure of fish on zooplankton. The [MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII] ratio can be used as a marker criterion for the evaluation of the trophy of a water body and its ecosystem and, particularly, for permanent monitoring of a water body. This ratio decreases with the rise of the trophic state (Gulati, 1983; Andronikova, 1996; Jeppesen et al., 1999, 2000, 2005; Haberman & Laugaste, 2003). It is widely recognized that phytoplankton is influenced most by nutrients (bottom up) while zooplankton is influenced both by consumers (top down) and algae (bottom up). This causes their different seasonal dynamics and complicated relevant ratios. Thus, the values of the [MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII] ratio are fluctuating within and across years. This variability has not been thoroughly analysed. Some data concerning this ratio for L. Peipsi have been published on the basis of plankton sampled up to the end of the last century (Haberman, 1996; Haberman & Laugaste, 2003; Noges & Noges, 2006). As the situation in the lake has changed markedly during this decade, a new analysis of the ratio has been initiated. About two decades ago, the ecosystem of the lake was in a quite good balance, and an effective algal food web prevailed in the open water (Noges et al., 1993). Since the late 1990s and during the 2000s, the ecosystem of the lake lost its stability. The proportion of cyanobacteria in the biomass of summer phytoplankton increased consistently: from 20% to 70% in L. Peipsi sensu stricto (s.s.), and from 30% to 90% in the southern lake parts (Laugaste et al., 2007). An appreciable concentration of microcystins was detected in the lake water in the summer months of the 2000s (Tanner et al., 2005), and the biomass of the genus Microcystis exceeded 20 g [m.sup.-3] in the southern lake parts in some years. At the same time, a continuous decline in zooplankton (Haberman et al., 2008) and changes in fish population (Kangur et al., 2008) were observed. The stock of planktivorous smelt (Osmerus eperlanus eperlanus m. spirinchus Pallas) and vendace (Coregonus albula (L.)) decreased drastically, and the abundance of piscivorous pikeperch (Stizostedion lucioperca (L.)) increased but, owing to over-fishing, the amount of pikeperch is modest (Kangur et al., 2008). Noges et al. (2005) explained the destabilization of the ecosystem with a decrease in the N : P ratio caused by increased phosphorus loading and reduced nitrogen loading in recent decades. The aim of this study was to follow the variations of the [MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII] ratio in different months, in different parts of the lake, and in different years; to establish boundaries of this variability, and to analyse how its changes reflect the state of the lake. We argue that the [MATHEMATICAL EXPRESSION NOT REPRODUCIBLE IN ASCII] ratio (particularly the mean for a growing season) can be used as a marker characteristic for estimating the trophy of a water body. STUDY SITE Lake Peipsi sensu lato (s.l.) is a large (area 3555 [km.sup.2], the fourth largest lake in Europe) and shallow (mean depth 7.1 m), mainly unstratified lowland water body. Located on the Estonian-Russian border, L. Peipsi is the largest trans boundary lake in Europe. …