Â© 2018, Springer International Publishing AG, part of Springer Nature. Coastal lagoon ecosystems are vulnerable to eutrophication, which leads to the accumulation of nutrients from the surrounding watershed over the long term. However, there is a lack of information about methods that could accurate quantify this problem in rapidly developed countries. Therefore, various statistical methods such as cluster analysis (CA), principal component analysis (PCA), partial least square (PLS), principal component regression (PCR), and ordinary least squares regression (OLS) were used in this study to estimate total organic matter content in sediments (TOM) using other parameters such as temperature, dissolved oxygen (DO), pH, electrical conductivity (EC), nitrite (NO 2 ), nitrate (NO 3 ), biological oxygen demand (BOD), phosphate (PO 4 ), total phosphorus (TP), salinity, and water depth along a 3-km transect in the Gomishan Lagoon (Iran). Results indicated that nutrient concentration and the dissolved oxygen gradient were the most significant parameters in the lagoon water quality heterogeneity. Additionally, anoxia at the bottom of the lagoon in sediments and re-suspension of the sediments were the main factors affecting internal nutrient loading. To validate the models, R 2 , RMSECV, and RPDCV were used. The PLS model was stronger than the other models. Also, classification analysis of the Gomishan Lagoon identified two hydrological zones: (i) a North Zone characterized by higher water exchange, higher dissolved oxygen and lower salinity and nutrients, and (ii) a Central and South Zone with high residence time, higher nutrient concentrations, lower dissolved oxygen, and higher salinity. A recommendation for the management of coastal lagoons, specifically the Gomishan Lagoon, to decrease or eliminate nutrient loadings is discussed and should be transferred to policy makers, the scientific community, and local inhabitants.