The moderately salty and lightly salty lakes and marshes near the Black Sea are specific in terms of their high degree of physical alteration; intensive hydromorphological pressure; and point-source and diffusive enrichment with biogenic, organic and inorganic compounds. Nutrients are among the most regularly measured variables in monitoring programs, providing the most complete information for long-term analysis and assessment. Nonetheless, their results need a final summary score, such as the water quality index, which assesses spatial and temporal conditions very well. In this study, we used all available data for Varna and Burgas Lakes from state monitoring for six years (2016–2021), using the parameters monitored with the greatest frequency. The aims were to trace temporal changes in the water quality parameters to determine which of the biogenic elements had the greatest significance for the variance in water quality while seeking the most contributing elements for the formation of the Canadian Council of Ministers of the Environment water quality index (CCME-WQI). The objectives were achieved via multiple factor analysis (MFA) loaded with the results for the environmental variables and the final scores of the CCME-WQI since this multivariate analysis allows simultaneous consideration of multiple data series while balancing the influence of each set of variables. MFA revealed that CCME-WQI scores were influenced solely by total phosphorus (TP) in Varna Lake, where TP was negatively correlated with total nitrogen. In Burgas Lake, TP had the greatest influence on the CCME-WQI, but in this slightly saline lake, pH and dissolved oxygen were also negatively correlated with the complex assessment scores. The approach developed in this study is simple to implement and provides information for the simultaneous use of both the CCME-WQI and the MFA, which could optimize monitoring programs by directing sampling efforts on fewer parameters that could be analyzed more often or from more sampling sites.