| Summary: | The post-soviet period in Eastern Europe brought about fast changes in economy, land use, and environmental protection, whereas legacy effects of the previous era of heavy contamination continued emerging in the status of water bodies. In this paper, we analysed the post-soviet (since 1992) changes in catchment nutrient loadings and stoichiometry of nitrogen (N) and phosphorus (P) in two large non-stratified lakes in Estonia – Võrtsjärv and Peipsi. The drastic reduction in the application of P-fertilisers and P discharges with wastewaters since the early 1990s reduced P loadings and increased N/P loading ratio into both lakes. However, it was hard to find clear evidence of reduced in-lake nutrient concentrations and improved water quality. In both lakes, water transparency constantly decreased and phytoplankton biomass increased. Over the years, the difference in N/P ratio between the two lakes became smaller while the large differences in the cyanobacterial community composition remained. Although common thresholds in nutrient ratios favouring N2-fixing species could be revealed in both lakes, the phytoplankton in Võrtsjärv, strongly dominated by Limnothrix spp., remained mostly light-limited and the relationship with N/P stoichiometry was indirect. Random Forest analysis indicated an important role of light limitation in both lakes. Constantly lower levels of N in the deeper Lake Peipsi favoured N2-fixing species, which, as a paradox, became P-limited. As climate warming reinforces eutrophication phenomena in lakes by increasing internal nutrient loading and favouring bloom-forming cyanobacteria, more stringent measures would be needed to further limit nutrient loads (especially that of P) to lakes through improved wastewater treatment and increased efficiency of fertiliser application.
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