Eastern Continental shallow lakes are specific with their higher nutrient concentration compared to other lentic water bodies with similar specifications. Nonetheless, their phytoplankton and macrophyte assessment systems used more often than others within state monitoring programs, are weakly influenced by nutrient concentrations, unlike all other lake types in Europe. In this study, we used all available data for Eastern Continental shallow lakes on the Black Sea coast of Bulgaria from the state monitoring for 14 years (2008-2021). The goal was to find how environmental variables influence the ecological status assessment by phytoplankton and macrophyte-related indices. Likewise, it was important to understand the studied parameter’s interrelations within Dourankoulak Lake and the lake complex Shabla-Ezerets. The most important environmental parameters were determined with principal component analysis since it helps find the hidden relationships. Afterwards, those variables were used for univariate linear regression testing because of its simplicity and reliability. The aim was to find the best-suited parameters for the ecological status explanation by different biological indices, which can be used for further predictions of the ecosystem condition. In addition, nitrogen–phosphorus dependency, where possible was investigated, confirming conclusions from mesocosms studies from water bodies with similar characteristics. The algae group index or the so-called “Catalán Index”, in its original form of representing results and considering its ecological quality ratio values, was influenced by conductivity concentrations the most in Ezeretsko Lake and weaker at Dourankoulak Lake. Nutrient relationship with biological quality elements was not found, confirming results on a European level. In Shablensko Lake a dose-dependent relation between nitrates and phosphates was found, which shows that augmenting the quantity of nitrogen is related to the increasing concentration of phosphates.