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The floating houses in Tonle Sap Lake might be one of the main factors for degradation of water quality since the people in floating houses discharge sewage and waste from their households into the lake. Therefore, the government of Cambodia has decided to move the floating houses in Chhnok Tru to the upland regions, and more than 90% of the floating houses in Chhnok Tru have already been moved in accordance with the government’s plan. However, the scientific information on water quality before and after moving the floating houses in Tonle Sap Lake is limited. Thus, this paper aimed to evaluate differences in basic water quality such as temperature, pH, dissolved oxygen (DO), oxidation–reduction potential (ORP), conductivity (Cond), and nitrate (NO3−) before and after the floating houses were moved and to reveal the relationships between the floating houses and basic water quality. The water quality parameters were measured at 18 sampling sites in Chhnok Tru using an EXO sensor and NO3− was analyzed by ion chromatography (IC). Statistical analyses such as t-tests, correlation analysis, principal component analysis (PCA), and structural equation modeling (SEM) were used. The results show that the water quality was better after moving the floating houses; however, some parts of the study area were still polluted. In addition, the percentage of floating house distribution was significantly correlated with the temperature and ORP in the study area during dry and wet seasons. The obtained results are useful for making management decisions to sustainably manage the water quality in the area.