In this study, the current status of water quality in Güllük Lagoon and Köyceğiz-Dalyan Lagoon was examined by comparison using water quality indexes, multivariate statistical analyses and geographical information systems. Water quality parameters comprised of 9 variables i.e., WT, pH, DO, NO2-N, NO3-N, NH4-N, TP, SSM, BOD5 were measured in Güllük Lagoon and Köyceğiz-Dalyan Lagoon. Although there are important activities such as earthen pond fish farms, fish hatcheries, feldsbat and marble quarries, streams carrying domestic wastes, port, secondary residences and agricultural activities in Güllük Lagoon, there are intense tourism and agricultural activities in Köyceğiz-Dalyan Lagoon. The average concentrations of DO, TP, NO2-N results in Güllük Lagoon and DO, TP and NH4-N results in Köyceğiz-Dalyan Lagoon were determined in second class water quality according to surface water quality criteria. While both lagoons were found to be in “Good” quality class as a result of water quality index, Güllük Lagoon was found to be “medium polluted” and Köyceğiz-Dalyan Lagoon was found to be “slightly polluted” quality class as a result of comprehensive pollution index. It was observed that water quality index values of both lagoons decreased in the dry season, while their comprehensive pollution index values increased in the dry season. On the basis of the general averages of water quality index, it was found as Köyceğiz-Dalyan Lagoon (85.0) > Güllük Lagoon (84.05), and on the basis of the general averages of comprehensive pollution index, it was found as Güllük Lagoon (1.34) > Köyceğiz-Dalyan Lagoon (0.79). Relationships between variables were determined by geographical information systems (IDW technique) and statistical analyses (Descriptive statistics, Spearman rho correlation, Kruskal-Wallis test, multiple linear regression and Principal component analysis). As a result of multiple linear regression analysis in measured parameters, it was determined that the most important parameter affecting the water quality index in Güllük Lagoon was NH4-N, and the most important parameter affecting the comprehensive pollution index was SSM. In Köyceğiz-Dalyan Lagoon, it was observed that the water quality index was affected by the WT parameter and the comprehensive pollution index was affected by the SSM parameter. There is no difference in the concentrations of the average water quality parameters measured in both lagoons, and both lagoons are generally in the first and second class surface water quality class. However, Güllük Lagoon, which contains more different pollutant sources than Köyceğiz-Dalyan Lagoon, is shown to be more polluted according to water quality indexes. In addition, it has been determined that SSM is the most important parameter that determines the water quality among the measured water quality parameters of both lagoons.
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